diff --git a/ChangeLog.md b/ChangeLog.md index 59fbbed641..efe91e9d23 100644 --- a/ChangeLog.md +++ b/ChangeLog.md @@ -1,5 +1,5 @@ -QIIME 1.8.0-dev (changes since 1.8.0 go here) -============================================= +QIIME 1.9.0-rc1 +=============== * Added new ``observation_metadata_correlation.py`` script. This script allows the calculation of correlations between feature abundances and continuous-valued metadata. This script replaces the continuous-valued correlation functionality that was in ``otu_category_significance.py`` in QIIME 1.7.0 and earlier. * ``split_otu_table.py`` now allows multiple fields to be passed to split a biom table, and optionally a mapping file. Check out the new documentation for the naming conventions @@ -101,6 +101,8 @@ optionally a mapping file. Check out the new documentation for the naming conven * Fixed bug that resulted in samples being mislabeled in ``make_otu_heatmap.py`` when one of the following options was passed: ``--category``, ``--map_fname``, ``--sample_tree``, or ``--suppress_column_clustering``. This is discussed in [#1790](https://github.com/biocore/qiime/issues/1790). * Added ``--negate_sample_id_fp`` option to ``filter_samples_from_otu_table.py`` (see [#1117](https://github.com/biocore/qiime/issues/1117)). * Added three new workflow scripts for facilitating initial QIIME processing of already-demultiplexed fastq files, as these are commonly being provided by sequencing centers. These are: ``multiple_split_libraries_fastq.py``, ``multiple_join_paired_ends.py``, and ``multiple_extract_barcodes.py``. +* Added ``differential_abundance.py`` to supplement ``group_significance.py`` for to support metagenomeSeq's fitZIG algorithm and DESeq2's negative binomial algorithm. Note that the input for this is a unnormalized, raw BIOM table. +* Added ``normalize_table.py`` to support normalization algorithms in addition to rarefaction. Supported methods are metagenomeSeq's CSS and DESeq's variance stabilizing transformation. QIIME 1.8.0 (11 Dec 2013) ========================= diff --git a/doc/conf.py b/doc/conf.py index ab91778312..cf6c8fabd4 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -46,9 +46,9 @@ # built documents. # # The short X.Y version. -version = '1.8.0-dev' +version = '1.9.0-rc1' # The full version, including alpha/beta/rc tags. -release = '1.8.0-dev' +release = '1.9.0-rc1' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/qiime/__init__.py b/qiime/__init__.py index 144e6e778d..024f6a4846 100644 --- a/qiime/__init__.py +++ b/qiime/__init__.py @@ -18,7 +18,7 @@ "Daniel McDonald", "Catherine Lozupone"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/add_alpha_to_mapping_file.py b/qiime/add_alpha_to_mapping_file.py index 0e2e38f9bb..e98c69d420 100755 --- a/qiime/add_alpha_to_mapping_file.py +++ b/qiime/add_alpha_to_mapping_file.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Yoshiki Vazquez-Baeza", "Antonio Gonzalez-Pena"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Yoshiki Vazquez-Baeza" __email__ = "yoshiki89@gmail.com" diff --git a/qiime/add_qiime_labels.py b/qiime/add_qiime_labels.py index bd788be54b..0bf7f91d13 100755 --- a/qiime/add_qiime_labels.py +++ b/qiime/add_qiime_labels.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters", "Emily TerAvest"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/qiime/adjust_seq_orientation.py b/qiime/adjust_seq_orientation.py index 1f115ea4d7..b3dd351be4 100755 --- a/qiime/adjust_seq_orientation.py +++ b/qiime/adjust_seq_orientation.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Antonio Gonzalez Pena"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/align_seqs.py b/qiime/align_seqs.py index 4660f38ef7..3b03fe15ed 100644 --- a/qiime/align_seqs.py +++ b/qiime/align_seqs.py @@ -8,7 +8,7 @@ "Jeremy Widmann", "Kyle Bittinger"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/alpha_diversity.py b/qiime/alpha_diversity.py index 99e297b3a7..d800654151 100644 --- a/qiime/alpha_diversity.py +++ b/qiime/alpha_diversity.py @@ -6,7 +6,7 @@ "William Van Treuren", "Jose Antonio Navas Molina", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/assign_taxonomy.py b/qiime/assign_taxonomy.py index ee33538e33..f99a8d5910 100644 --- a/qiime/assign_taxonomy.py +++ b/qiime/assign_taxonomy.py @@ -7,7 +7,7 @@ __credits__ = ["Rob Knight", "Greg Caporaso", "Kyle Bittinger", "Antonio Gonzalez Pena", "David Soergel", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/barcode.py b/qiime/barcode.py index ed989a10f8..7567838512 100644 --- a/qiime/barcode.py +++ b/qiime/barcode.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] # remember to add yourself __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/beta_diversity.py b/qiime/beta_diversity.py index 3cae13688a..d874ced1b6 100644 --- a/qiime/beta_diversity.py +++ b/qiime/beta_diversity.py @@ -6,7 +6,7 @@ "Jose Carlos Clemente Litran", "Jai Ram Rideout", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/beta_metrics.py b/qiime/beta_metrics.py index c603a74817..ca0309de5e 100644 --- a/qiime/beta_metrics.py +++ b/qiime/beta_metrics.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Rob Knight", "Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/biplots.py b/qiime/biplots.py index 1c7ee2ee74..7b39b2cd55 100644 --- a/qiime/biplots.py +++ b/qiime/biplots.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Dan Knights", "Justin Kuczynski"] # remember to add yourself __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Dan Knights" __email__ = "daniel.knights@colorado.edu" diff --git a/qiime/categorized_dist_scatterplot.py b/qiime/categorized_dist_scatterplot.py index acbcf61151..9224063879 100755 --- a/qiime/categorized_dist_scatterplot.py +++ b/qiime/categorized_dist_scatterplot.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/check_id_map.py b/qiime/check_id_map.py index 6729ea5a6e..1d4070a494 100644 --- a/qiime/check_id_map.py +++ b/qiime/check_id_map.py @@ -43,7 +43,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Rob Knight", "William Walters"] # remember to add yourself __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Walters" __email__ = "william.a.walters@colorado.edu" diff --git a/qiime/clean_raxml_parsimony_tree.py b/qiime/clean_raxml_parsimony_tree.py index 8c3f54394e..cd97705c3d 100644 --- a/qiime/clean_raxml_parsimony_tree.py +++ b/qiime/clean_raxml_parsimony_tree.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Jesse Stombaugh"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/qiime/cluster_quality.py b/qiime/cluster_quality.py index b07f6f0d7f..e1f4377e72 100644 --- a/qiime/cluster_quality.py +++ b/qiime/cluster_quality.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" """ computes cluster quality the default way, bet/within""" diff --git a/qiime/collate_alpha.py b/qiime/collate_alpha.py index 0af6bf9825..7d2adc4607 100644 --- a/qiime/collate_alpha.py +++ b/qiime/collate_alpha.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/colors.py b/qiime/colors.py index 3401d3cb2d..e078127e30 100644 --- a/qiime/colors.py +++ b/qiime/colors.py @@ -6,7 +6,7 @@ # remember to add yourself __credits__ = ["Rob Knight", "Jesse Stombaugh", "Yoshiki Vazquez-Baeza"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/qiime/compare_alpha_diversity.py b/qiime/compare_alpha_diversity.py index 58fd9d00dc..2f50185d91 100644 --- a/qiime/compare_alpha_diversity.py +++ b/qiime/compare_alpha_diversity.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["William Van Treuren", "Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Van Treuren" __email__ = "vantreur@colorado.edu" diff --git a/qiime/compare_categories.py b/qiime/compare_categories.py index db48c11c32..b89872e8c3 100755 --- a/qiime/compare_categories.py +++ b/qiime/compare_categories.py @@ -6,7 +6,7 @@ __credits__ = ["Jai Ram Rideout", "Michael Dwan", "Logan Knecht", "Damien Coy", "Levi McCracken"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/qiime/compare_distance_matrices.py b/qiime/compare_distance_matrices.py index a285ee53bb..ebf073b23f 100755 --- a/qiime/compare_distance_matrices.py +++ b/qiime/compare_distance_matrices.py @@ -6,7 +6,7 @@ __credits__ = ["Jai Ram Rideout", "Michael Dwan", "Logan Knecht", "Damien Coy", "Levi McCracken", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/qiime/compare_taxa_summaries.py b/qiime/compare_taxa_summaries.py index 72487990fc..08fc788e7e 100755 --- a/qiime/compare_taxa_summaries.py +++ b/qiime/compare_taxa_summaries.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2012, The QIIME project" __credits__ = ["Jai Ram Rideout", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/qiime/compare_trajectories.py b/qiime/compare_trajectories.py index 0a035220e6..a466893d10 100644 --- a/qiime/compare_trajectories.py +++ b/qiime/compare_trajectories.py @@ -5,7 +5,7 @@ __credits__ = ["Jose Antonio Navas Molina", "Antonio Gonzalez Pena", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jose Antonio Navas Molina" __email__ = "josenavasmolina@gmail.com" diff --git a/qiime/compute_taxonomy_ratios.py b/qiime/compute_taxonomy_ratios.py index 99147c6edc..94eff52960 100644 --- a/qiime/compute_taxonomy_ratios.py +++ b/qiime/compute_taxonomy_ratios.py @@ -11,7 +11,7 @@ __copyright__ = "Copyright 2014, The QIIME project" __credits__ = ["Daniel McDonald"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Daniel McDonald" __email__ = "mcdonadt@colorado.edu" diff --git a/qiime/convert_fastaqual_fastq.py b/qiime/convert_fastaqual_fastq.py index c679a03994..69ddeff7e9 100644 --- a/qiime/convert_fastaqual_fastq.py +++ b/qiime/convert_fastaqual_fastq.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Adam Robbins-Pianka, Abhisaar Yadav"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Adam Robbins-Pianka" __email__ = "adam.robbinspianka@colorado.edu" diff --git a/qiime/core_microbiome.py b/qiime/core_microbiome.py index 9cf57212f4..af568d7ddc 100644 --- a/qiime/core_microbiome.py +++ b/qiime/core_microbiome.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/demultiplex_fasta.py b/qiime/demultiplex_fasta.py index 704d39af90..4cf7921265 100755 --- a/qiime/demultiplex_fasta.py +++ b/qiime/demultiplex_fasta.py @@ -13,7 +13,7 @@ "Jens Reeder", "Emily TerAvest"] # remember to add yourself __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Walters" __email__ = "william.a.walters@colorado.edu" diff --git a/qiime/denoise_wrapper.py b/qiime/denoise_wrapper.py index 31c79a0e5f..0a4059faf9 100644 --- a/qiime/denoise_wrapper.py +++ b/qiime/denoise_wrapper.py @@ -7,7 +7,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jens Reeder", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/denoiser/__init__.py b/qiime/denoiser/__init__.py index 6ea5e5a3a5..2b6adf3ef4 100644 --- a/qiime/denoiser/__init__.py +++ b/qiime/denoiser/__init__.py @@ -5,7 +5,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/qiime/denoiser/cluster_utils.py b/qiime/denoiser/cluster_utils.py index 573028f2d5..b2a706bd58 100644 --- a/qiime/denoiser/cluster_utils.py +++ b/qiime/denoiser/cluster_utils.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight", "Nigel Cook", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/qiime/denoiser/denoise_postprocess.py b/qiime/denoiser/denoise_postprocess.py index 3d14514ff3..d3e9fd5174 100644 --- a/qiime/denoiser/denoise_postprocess.py +++ b/qiime/denoiser/denoise_postprocess.py @@ -5,7 +5,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/qiime/denoiser/denoise_worker.py b/qiime/denoiser/denoise_worker.py index b80da8b5e6..a74f4430dd 100644 --- a/qiime/denoiser/denoise_worker.py +++ b/qiime/denoiser/denoise_worker.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight", "Nigel Cook"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/qiime/denoiser/flowgram_clustering.py b/qiime/denoiser/flowgram_clustering.py index 513ba39a35..c6711957e1 100644 --- a/qiime/denoiser/flowgram_clustering.py +++ b/qiime/denoiser/flowgram_clustering.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight", "Nigel Cook", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/qiime/denoiser/flowgram_filter.py b/qiime/denoiser/flowgram_filter.py index 9edfc9da91..9d1411a969 100644 --- a/qiime/denoiser/flowgram_filter.py +++ b/qiime/denoiser/flowgram_filter.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/qiime/denoiser/make_cluster_jobs.py b/qiime/denoiser/make_cluster_jobs.py index 4c7ec2b85f..359fb5a4c4 100755 --- a/qiime/denoiser/make_cluster_jobs.py +++ b/qiime/denoiser/make_cluster_jobs.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/qiime/denoiser/preprocess.py b/qiime/denoiser/preprocess.py index 1e82384445..26119b281e 100644 --- a/qiime/denoiser/preprocess.py +++ b/qiime/denoiser/preprocess.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/qiime/denoiser/utils.py b/qiime/denoiser/utils.py index 759fb13fa3..efb45b472c 100644 --- a/qiime/denoiser/utils.py +++ b/qiime/denoiser/utils.py @@ -8,7 +8,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/qiime/detrend.py b/qiime/detrend.py index de549d9124..485016151b 100644 --- a/qiime/detrend.py +++ b/qiime/detrend.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2012, The QIIME Project" __credits__ = ["Dan Knights", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Dan Knights" __email__ = "danknights@gmail.com" diff --git a/qiime/differential_abundance.py b/qiime/differential_abundance.py new file mode 100755 index 0000000000..b4105b5f36 --- /dev/null +++ b/qiime/differential_abundance.py @@ -0,0 +1,134 @@ +#!/usr/bin/env python +# File created on 14 Jul 2014 +from __future__ import division + +from os.path import exists, splitext, join, isdir +from os import makedirs, listdir, remove, path + +from qiime.parse import parse_mapping_file_to_dict +from qiime.util import RExecutor +from biom import load_table + + +__author__ = "Sophie Weiss" +__copyright__ = "Copyright 2014, The QIIME Project" +__credits__ = ["Sophie Weiss", "Joseph Paulson"] +__license__ = "GPL" +__version__ = "1.9.0-rc1" +__maintainer__ = "Sophie Weiss" +__email__ = "sophie.sjw@gmail.com" + + + +def DA_fitZIG(input_path, out_path, mapping_fp, mapping_category, subcategory_1, subcategory_2): + """perform metagenomeSeq's Zero Inflated Gaussian (ZIG) OTU differential abundance testing""" + base_fname, ext = splitext(input_path) + json_infile = base_fname+'_json.biom' + tmp_bt = load_table(input_path) + tmp_pmf, _ = parse_mapping_file_to_dict(mapping_fp) + tmp_bt.add_metadata(tmp_pmf, 'sample') + open(str(json_infile),'w').write(tmp_bt.to_json('forR')) + + run_fitZIG(json_infile, out_path, mapping_category, subcategory_1, subcategory_2) + remove(json_infile) + + +def multiple_file_DA_fitZIG(input_dir, output_dir, mapping_fp, mapping_category, subcategory_1, subcategory_2): + """perform metagenomeSeq's Zero Inflated Gaussian (ZIG) OTU differential abundance test on a directory of raw abundance OTU matrices + """ + if not exists(output_dir): + makedirs(output_dir) + file_names = [fname for fname in listdir(input_dir) if not (fname.startswith('.')\ + or isdir(fname))] + + for fname in file_names: + base_fname, ext = splitext(fname) + original_fname = base_fname+'.biom' + json_fname = base_fname+'_json.biom' + hdf5_infile = join(input_dir, original_fname) + json_infile = join(input_dir, json_fname) + tmp_bt = load_table(hdf5_infile) + tmp_pmf, _ = parse_mapping_file_to_dict(mapping_fp) + tmp_bt.add_metadata(tmp_pmf, 'sample') + #make temporary json biom version - R currently does not have hdf5 + open(str(json_infile),'w').write(tmp_bt.to_json('forR')) + outfile = join(output_dir, 'fitZIG_DA_'+base_fname+'.txt') + + run_fitZIG(json_infile, outfile, mapping_category, subcategory_1, subcategory_2) + remove(json_infile) + + +def run_fitZIG(input_path, out_path, mapping_category, subcategory_1, subcategory_2, HALT_EXEC=False): + """Run metagenomeSeq's fitZIG algorithm through Rscript + """ + # set options + command_args = ['-i %s -o %s -c %s -x %s -y %s' % (input_path, out_path, mapping_category, subcategory_1, subcategory_2)] + # instantiate the object + rsl = RExecutor() + # run the app + app_result = rsl(command_args=command_args, script_name='fitZIG.r') + + return app_result + + +def DA_DESeq2(input_path, out_path, mapping_fp, mapping_category, subcategory_1, subcategory_2, DESeq2_diagnostic_plots): + """perform DESeq2 negative binomial differential abundance test on a raw abundance OTU matrix + """ + base_fname, ext = splitext(input_path) + json_infile = base_fname+'_json.biom' + tmp_bt = load_table(input_path) + tmp_pmf, _ = parse_mapping_file_to_dict(mapping_fp) + tmp_bt.add_metadata(tmp_pmf, 'sample') + open(str(json_infile),'w').write(tmp_bt.to_json('forR')) + base_fname, ext = splitext(out_path) + outfile_diagnostic = join(base_fname+'_diagnostic_plots.pdf') + + run_DESeq2(json_infile, out_path, mapping_category, subcategory_1, subcategory_2, DESeq2_diagnostic_plots, outfile_diagnostic) + remove(json_infile) + + +def multiple_file_DA_DESeq2(input_dir, output_dir, mapping_fp, mapping_category, subcategory_1, subcategory_2, DESeq2_diagnostic_plots): + """perform DESeq2 negative binomial differential abundance test on a directory of raw abundance OTU matrices + """ + if not exists(output_dir): + makedirs(output_dir) + file_names = [fname for fname in listdir(input_dir) if not (fname.startswith('.')\ + or isdir(fname))] + + for fname in file_names: + base_fname, ext = splitext(fname) + original_fname = base_fname+'.biom' + json_fname = base_fname+'_json.biom' + hdf5_infile = join(input_dir, original_fname) + json_infile = join(input_dir, json_fname) + tmp_bt = load_table(hdf5_infile) + tmp_pmf, _ = parse_mapping_file_to_dict(mapping_fp) + tmp_bt.add_metadata(tmp_pmf, 'sample') + open(str(json_infile),'w').write(tmp_bt.to_json('forR')) + outfile = join(output_dir, 'DESeq2_DA_'+base_fname+'.txt') + outfile_diagnostic = join(output_dir, 'DESeq2_diagnostic_plots_'+base_fname+'.pdf') + + run_DESeq2(json_infile, outfile, mapping_category, subcategory_1, subcategory_2, DESeq2_diagnostic_plots, outfile_diagnostic) + remove(json_infile) + + +def run_DESeq2(input_path, out_path, mapping_category, subcategory_1, subcategory_2, DESeq2_diagnostic_plots, outfile_diagnostic, HALT_EXEC=False): + """Run metagenomeSeq's fitZIG algorithm through Rscript + """ + # set options + if DESeq2_diagnostic_plots==True: + command_args = ['-i %s -o %s -c %s -x %s -y %s -d %s -e %s' % (input_path, out_path, mapping_category, subcategory_1, subcategory_2, DESeq2_diagnostic_plots, outfile_diagnostic)] + else: + command_args = ['-i %s -o %s -c %s -x %s -y %s' % (input_path, out_path, mapping_category, subcategory_1, subcategory_2)] + # instantiate the object + rsl = RExecutor() + # run the app + app_result = rsl(command_args=command_args, script_name='DESeq2_nbinom.r') + + return app_result + + +def algorithm_list(): + """ returns list of differential abundance detection algorithms from qiime.differential_abundance + """ + return ['metagenomeSeq_fitZIG', 'DESeq2_nbinom'] \ No newline at end of file diff --git a/qiime/distance_matrix_from_mapping.py b/qiime/distance_matrix_from_mapping.py index bda50f4928..3951047268 100644 --- a/qiime/distance_matrix_from_mapping.py +++ b/qiime/distance_matrix_from_mapping.py @@ -7,7 +7,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Antonio Gonzalez Pena", "Andrew J. King"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Antonio Gonzalez Pena" __email__ = "antgonza@gmail.com" diff --git a/qiime/estimate_observation_richness.py b/qiime/estimate_observation_richness.py index 39b9d832fe..64d7cd27d8 100755 --- a/qiime/estimate_observation_richness.py +++ b/qiime/estimate_observation_richness.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2013, The QIIME Project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/qiime/exclude_seqs_by_blast.py b/qiime/exclude_seqs_by_blast.py index c90b19c929..2d754ba84c 100644 --- a/qiime/exclude_seqs_by_blast.py +++ b/qiime/exclude_seqs_by_blast.py @@ -17,7 +17,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jesse Zaneveld", "Rob Knight", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jesse Zaneveld" __email__ = "zaneveld@gmail.com" diff --git a/qiime/extract_barcodes.py b/qiime/extract_barcodes.py index 59872c4e8b..3beec47a73 100644 --- a/qiime/extract_barcodes.py +++ b/qiime/extract_barcodes.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters", "Daniel McDonald"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Walters" __email__ = "william.a.walters@gmail.com" diff --git a/qiime/filter.py b/qiime/filter.py index de61488b2c..ace45d3e9a 100644 --- a/qiime/filter.py +++ b/qiime/filter.py @@ -7,7 +7,7 @@ __credits__ = ["Greg Caporaso", "Will Van Treuren", "Daniel McDonald", "Jai Ram Rideout", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/filter_alignment.py b/qiime/filter_alignment.py index f0b57fc448..b9ec0ae926 100755 --- a/qiime/filter_alignment.py +++ b/qiime/filter_alignment.py @@ -20,7 +20,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Justin Kuczynski", "Dan Knights"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/filter_otus_by_sample.py b/qiime/filter_otus_by_sample.py index 02f84e1a64..a2a9a0bb97 100644 --- a/qiime/filter_otus_by_sample.py +++ b/qiime/filter_otus_by_sample.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jesse Stombaugh"] # remember to add yourself __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/qiime/format.py b/qiime/format.py index 9789479ecd..21456af3e2 100755 --- a/qiime/format.py +++ b/qiime/format.py @@ -6,7 +6,7 @@ "Antonio Gonzalez Pena", "Daniel McDonald", "Jai Ram Rideout"] # remember to add yourself if you make changes __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/golay.py b/qiime/golay.py index 54474fe0c3..e975475aa7 100644 --- a/qiime/golay.py +++ b/qiime/golay.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/group.py b/qiime/group.py index c4ec40b340..17d27789be 100755 --- a/qiime/group.py +++ b/qiime/group.py @@ -8,7 +8,7 @@ "Greg Caporaso", "Jeremy Widmann"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/qiime/hamming.py b/qiime/hamming.py index 8ef68847e2..d9fa3e01f9 100644 --- a/qiime/hamming.py +++ b/qiime/hamming.py @@ -15,7 +15,7 @@ # remember to add yourself if you make changes __credits__ = ["Micah Hamady", "Rob Knight"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/hierarchical_cluster.py b/qiime/hierarchical_cluster.py index 9e465c2efd..962e896387 100644 --- a/qiime/hierarchical_cluster.py +++ b/qiime/hierarchical_cluster.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/identify_chimeric_seqs.py b/qiime/identify_chimeric_seqs.py index 5a1fa2e833..a3dc93d53a 100755 --- a/qiime/identify_chimeric_seqs.py +++ b/qiime/identify_chimeric_seqs.py @@ -28,7 +28,7 @@ __credits__ = ["Greg Caporaso", "Jens Reeder", "William Walters", "Jai Ram Rideout", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/join_paired_ends.py b/qiime/join_paired_ends.py index a9d935c739..f981a4f826 100644 --- a/qiime/join_paired_ends.py +++ b/qiime/join_paired_ends.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2013, The QIIME Project" __credits__ = ["Mike Robeson"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Mike Robeson" __email__ = "robesonms@ornl.gov" diff --git a/qiime/make_2d_plots.py b/qiime/make_2d_plots.py index 99690ef350..80b2bc2b60 100644 --- a/qiime/make_2d_plots.py +++ b/qiime/make_2d_plots.py @@ -7,7 +7,7 @@ # remember to add yourself __credits__ = ["Jesse Stombaugh", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/qiime/make_bipartite_network.py b/qiime/make_bipartite_network.py index 738c24ce9c..ff3d34d032 100644 --- a/qiime/make_bipartite_network.py +++ b/qiime/make_bipartite_network.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2013, The QIIME Project" __credits__ = ["Will Van Treuren, Julia Goodrich"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Will Van Treuren" __email__ = "wdwvt1@gmail.com" diff --git a/qiime/make_bootstrapped_tree.py b/qiime/make_bootstrapped_tree.py index 43287bebb5..30015e1f89 100644 --- a/qiime/make_bootstrapped_tree.py +++ b/qiime/make_bootstrapped_tree.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/make_distance_boxplots.py b/qiime/make_distance_boxplots.py index c31f04c8ba..4ccd6f09a8 100755 --- a/qiime/make_distance_boxplots.py +++ b/qiime/make_distance_boxplots.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2012, The QIIME project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/qiime/make_fastq.py b/qiime/make_fastq.py index 6854fe8ae2..ee22269e2e 100644 --- a/qiime/make_fastq.py +++ b/qiime/make_fastq.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Rob Knight"] # remember to add yourself if you make changes __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/qiime/make_library_id_lists.py b/qiime/make_library_id_lists.py index 469f22d5b8..ff11d3269a 100644 --- a/qiime/make_library_id_lists.py +++ b/qiime/make_library_id_lists.py @@ -10,7 +10,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Rob Knight"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/qiime/make_otu_heatmap.py b/qiime/make_otu_heatmap.py index e82493c68f..b94a7f5500 100644 --- a/qiime/make_otu_heatmap.py +++ b/qiime/make_otu_heatmap.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Dan Knights", "Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Dan Knights" __email__ = "daniel.knights@colorado.edu" diff --git a/qiime/make_otu_network.py b/qiime/make_otu_network.py index 085fd60c24..fe49ed1fa5 100644 --- a/qiime/make_otu_network.py +++ b/qiime/make_otu_network.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Julia Goodrich"] # remember to add yourself __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jose Clemente" __email__ = "jose.clemente@gmail.com" diff --git a/qiime/make_otu_table.py b/qiime/make_otu_table.py index 26a6320896..0f70d0f518 100644 --- a/qiime/make_otu_table.py +++ b/qiime/make_otu_table.py @@ -5,7 +5,7 @@ __credits__ = ["Rob Knight", "Justin Kuczynski", "Adam Robbins-Pianka", "Sami Pietila"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/make_per_library_sff.py b/qiime/make_per_library_sff.py index a878b0c04c..b4c10d478f 100644 --- a/qiime/make_per_library_sff.py +++ b/qiime/make_per_library_sff.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Kyle Bittinger"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/qiime/make_phylogeny.py b/qiime/make_phylogeny.py index 9ba721ee75..dfae6cade5 100644 --- a/qiime/make_phylogeny.py +++ b/qiime/make_phylogeny.py @@ -5,7 +5,7 @@ __credits__ = ["Rob Knight", "Justin Kuczynski", "Daniel McDonald", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/make_rarefaction_plots.py b/qiime/make_rarefaction_plots.py index 4cfc1bc98f..6b69a63209 100644 --- a/qiime/make_rarefaction_plots.py +++ b/qiime/make_rarefaction_plots.py @@ -7,7 +7,7 @@ "Will Van Treuren", "Yoshiki Vazquez Baeza", "Jai Ram Rideout", "Evan Bolyen"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/qiime/map_reads_to_reference.py b/qiime/map_reads_to_reference.py index 7143236488..63d49d8e76 100644 --- a/qiime/map_reads_to_reference.py +++ b/qiime/map_reads_to_reference.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/nmds.py b/qiime/nmds.py index 2f11b51b95..1b2b31c4ea 100644 --- a/qiime/nmds.py +++ b/qiime/nmds.py @@ -10,7 +10,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/normalize_table.py b/qiime/normalize_table.py new file mode 100755 index 0000000000..b1be901416 --- /dev/null +++ b/qiime/normalize_table.py @@ -0,0 +1,124 @@ +#!/usr/bin/env python +# File created on 14 Jul 2014 +from __future__ import division + +from os.path import exists, splitext, join, isdir +from os import makedirs, listdir, remove +from qiime.util import RExecutor +from biom import load_table + +__author__ = "Sophie Weiss" +__copyright__ = "Copyright 2014, The QIIME Project" +__credits__ = ["Sophie Weiss", "Joseph Paulson"] +__license__ = "GPL" +__version__ = "1.9.0-rc1" +__maintainer__ = "Sophie Weiss" +__email__ = "sophie.sjw@gmail.com" + + + +def normalize_CSS(input_path, out_path, output_CSS_statistics): + """performs metagenomeSeq's CSS normalization on a single raw abundance OTU matrix + """ + base_fname, ext = splitext(input_path) + json_infile = base_fname+'_json.biom' + open(str(json_infile),'w').write(load_table(input_path).to_json('forR')) + + if output_CSS_statistics: + base_fname, ext = splitext(out_path) + output_CSS_statistics = base_fname+'_CSS_statistics.txt' + + run_CSS(json_infile, out_path, output_CSS_statistics=output_CSS_statistics) + remove(json_infile) + + +def multiple_file_normalize_CSS(input_dir, output_dir, output_CSS_statistics): + """performs metagenomeSeq's CSS normalization on a directory of raw abundance OTU matrices + """ + if not exists(output_dir): + makedirs(output_dir) + file_names = [fname for fname in listdir(input_dir) if not (fname.startswith('.')\ + or isdir(fname))] + + for fname in file_names: + base_fname, ext = splitext(fname) + print base_fname + original_fname = base_fname+'.biom' + json_fname = base_fname+'_json.biom' + hdf5_infile = join(input_dir, original_fname) + json_infile = join(input_dir, json_fname) + open(str(json_infile),'w').write(load_table(hdf5_infile).to_json('forR')) + outfile = join(output_dir, 'CSS_'+base_fname+'.biom') + if output_CSS_statistics: + output_CSS_statistics = join(output_dir, 'CSS_statistics_'+base_fname+'.txt') + run_CSS(json_infile, outfile, output_CSS_statistics=output_CSS_statistics) + remove(json_infile) + +def run_CSS(input_path, out_path, output_CSS_statistics, HALT_EXEC=False): + """Run metagenomeSeq's fitZIG algorithm through Rscript + """ + # set options + if not output_CSS_statistics: + command_args = ['-i %s -o %s' % (input_path, out_path)] + else: + command_args = ['-i %s -o %s -s %s' % (input_path, out_path, output_CSS_statistics)] + # instantiate the object + rsl = RExecutor() + # run the app + app_result = rsl(command_args=command_args, script_name='CSS.r') + + return app_result + + +def normalize_DESeq(input_path, out_path, DESeq_negatives_to_zero): + """performs DESeqVS normalization on a single raw abundance OTU matrix + """ + base_fname, ext = splitext(out_path) + json_infile = base_fname+'_json.biom' + open(str(json_infile),'w').write(load_table(input_path).to_json('forR')) + + run_DESeq(json_infile, out_path, DESeq_negatives_to_zero) + remove(json_infile) + +def multiple_file_normalize_DESeq(input_dir, output_dir, DESeq_negatives_to_zero): + """performs DESeqVS normalization on a directory of raw abundance OTU matrices + """ + if not exists(output_dir): + makedirs(output_dir) + file_names = [fname for fname in listdir(input_dir) if not (fname.startswith('.')\ + or isdir(fname))] + + for fname in file_names: + base_fname, ext = splitext(fname) + original_fname = base_fname+'.biom' + json_fname = base_fname+'_json.biom' + hdf5_infile = join(input_dir, original_fname) + json_infile = join(input_dir, json_fname) + open(str(json_infile),'w').write(load_table(hdf5_infile).to_json('forR')) + outfile = join(output_dir, 'DESeqVS_'+base_fname+'.biom') + + run_DESeq(json_infile, outfile, DESeq_negatives_to_zero) + remove(json_infile) + +def run_DESeq(input_path, out_path, DESeq_negatives_to_zero, HALT_EXEC=False): + """Run metagenomeSeq's fitZIG algorithm through Rscript + """ + # set options + if DESeq_negatives_to_zero: + command_args = ['-i %s -o %s -z %s' % (input_path, out_path, DESeq_negatives_to_zero)] + else: + command_args = ['-i %s -o %s' % (input_path, out_path)] + # instantiate the object + rsl = RExecutor() + # run the app + app_result = rsl(command_args=command_args, script_name='DESeq2.r') + + return app_result + +def algorithm_list(): + """ returns list of normalization algorithms from qiime.normalize_table + """ + return ['CSS', 'DESeq'] + +if __name__ == "__main__": + main() diff --git a/qiime/otu_significance.py b/qiime/otu_significance.py index be0e6c2abc..71143a2aea 100644 --- a/qiime/otu_significance.py +++ b/qiime/otu_significance.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2013, The QIIME project" __credits__ = ["Will Van Treuren", "Luke Ursell", "Catherine Lozupone"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Luke Ursell" __email__ = "lkursell@gmail.com" diff --git a/qiime/parallel/__init__.py b/qiime/parallel/__init__.py index d301fad738..e955bf5970 100644 --- a/qiime/parallel/__init__.py +++ b/qiime/parallel/__init__.py @@ -20,7 +20,7 @@ "Daniel McDonald", "Catherine Lozupone"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/parallel/align_seqs.py b/qiime/parallel/align_seqs.py index 0a2e42cae4..69fcf119a3 100644 --- a/qiime/parallel/align_seqs.py +++ b/qiime/parallel/align_seqs.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/parallel/alpha_diversity.py b/qiime/parallel/alpha_diversity.py index 8ac8b1a34c..0841fc8555 100644 --- a/qiime/parallel/alpha_diversity.py +++ b/qiime/parallel/alpha_diversity.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/parallel/assign_taxonomy.py b/qiime/parallel/assign_taxonomy.py index 9ac2c5dbf2..e7ba01ff95 100644 --- a/qiime/parallel/assign_taxonomy.py +++ b/qiime/parallel/assign_taxonomy.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2012, The QIIME project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/qiime/parallel/beta_diversity.py b/qiime/parallel/beta_diversity.py index 83cd9c794a..ade9d03b83 100644 --- a/qiime/parallel/beta_diversity.py +++ b/qiime/parallel/beta_diversity.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/parallel/blast.py b/qiime/parallel/blast.py index 8be354b74a..4efa4b0f83 100755 --- a/qiime/parallel/blast.py +++ b/qiime/parallel/blast.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2012, The QIIME project" __credits__ = ["Jai Ram Rideout", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/qiime/parallel/identify_chimeric_seqs.py b/qiime/parallel/identify_chimeric_seqs.py index ce1e1a36d2..5b58698f5f 100755 --- a/qiime/parallel/identify_chimeric_seqs.py +++ b/qiime/parallel/identify_chimeric_seqs.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2012, The QIIME project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/qiime/parallel/map_reads_to_reference.py b/qiime/parallel/map_reads_to_reference.py index 1ddaedb1bb..199c1ff833 100644 --- a/qiime/parallel/map_reads_to_reference.py +++ b/qiime/parallel/map_reads_to_reference.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/parallel/merge_otus.py b/qiime/parallel/merge_otus.py index 7db8acc86a..16bec04b63 100644 --- a/qiime/parallel/merge_otus.py +++ b/qiime/parallel/merge_otus.py @@ -10,7 +10,7 @@ __copyright__ = "Copyright 2013, The QIIME Project" __credits__ = ["Daniel McDonald", "Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Daniel McDonald" __email__ = "mcdonadt@colorado.edu" diff --git a/qiime/parallel/multiple_rarefactions.py b/qiime/parallel/multiple_rarefactions.py index e86bcee458..c875363cb9 100644 --- a/qiime/parallel/multiple_rarefactions.py +++ b/qiime/parallel/multiple_rarefactions.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/parallel/pick_otus.py b/qiime/parallel/pick_otus.py index bc4256798a..03ccabe892 100644 --- a/qiime/parallel/pick_otus.py +++ b/qiime/parallel/pick_otus.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Jens Reeder", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/parallel/poller.py b/qiime/parallel/poller.py index d7ab27338d..5ad807eb3a 100755 --- a/qiime/parallel/poller.py +++ b/qiime/parallel/poller.py @@ -13,7 +13,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/parallel/util.py b/qiime/parallel/util.py index 0dc1a0d94d..3ea88ab39d 100644 --- a/qiime/parallel/util.py +++ b/qiime/parallel/util.py @@ -7,7 +7,7 @@ __credits__ = ["Greg Caporaso", "Jens Reeder", "Jai Ram Rideout", "Daniel McDonald"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/parse.py b/qiime/parse.py index 967944b031..be3a9027b9 100644 --- a/qiime/parse.py +++ b/qiime/parse.py @@ -8,7 +8,7 @@ "Antonio Gonzalez Pena", "Jai Ram Rideout", "Will Van Treuren", "Yoshiki Vazquez-Baeza", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/pick_otus.py b/qiime/pick_otus.py index 74e1f05066..31165f2430 100644 --- a/qiime/pick_otus.py +++ b/qiime/pick_otus.py @@ -5,7 +5,7 @@ "William Walters", "Jose Carlos Clemente Litran", "Adam Robbins-Pianka", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/pick_rep_set.py b/qiime/pick_rep_set.py index 421ff30a16..303959ef30 100644 --- a/qiime/pick_rep_set.py +++ b/qiime/pick_rep_set.py @@ -5,7 +5,7 @@ __credits__ = ["Rob Knight", "Greg Caporaso", "Kyle Bittinger", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Daniel McDonald" __email__ = "wasade@gmail.com" diff --git a/qiime/plot_rank_abundance_graph.py b/qiime/plot_rank_abundance_graph.py index 6e6dd12441..814c1660f6 100644 --- a/qiime/plot_rank_abundance_graph.py +++ b/qiime/plot_rank_abundance_graph.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jens Reeder", "Emily TerAvest"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/plot_semivariogram.py b/qiime/plot_semivariogram.py index 008786f7af..960c6ed5de 100644 --- a/qiime/plot_semivariogram.py +++ b/qiime/plot_semivariogram.py @@ -13,7 +13,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Antonio Gonzalez Pena"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Antonio Gonzalez Pena" __email__ = "antgonza@gmail.com" diff --git a/qiime/plot_taxa_summary.py b/qiime/plot_taxa_summary.py index 63a865f08b..eb918faeea 100644 --- a/qiime/plot_taxa_summary.py +++ b/qiime/plot_taxa_summary.py @@ -7,7 +7,7 @@ __credits__ = ["Jesse Stobmaugh", "Julia Goodrich", "Micah Hamady"] # remember to add yourself __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/qiime/principal_coordinates.py b/qiime/principal_coordinates.py index fc4983f689..43cbab0554 100644 --- a/qiime/principal_coordinates.py +++ b/qiime/principal_coordinates.py @@ -8,7 +8,7 @@ "Catherine Lozupone", "Emily TerAvest", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/process_sff.py b/qiime/process_sff.py index 2992dfe6d4..53cc8fbddf 100644 --- a/qiime/process_sff.py +++ b/qiime/process_sff.py @@ -29,7 +29,7 @@ "Adam Robbins-Pianka", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/qiime/pycogent_backports/__init__.py b/qiime/pycogent_backports/__init__.py index 0f5ddb18c7..bc5d2790ec 100644 --- a/qiime/pycogent_backports/__init__.py +++ b/qiime/pycogent_backports/__init__.py @@ -18,6 +18,6 @@ "Daniel McDonald", "Catherine Lozupone"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/quality_scores_plot.py b/qiime/quality_scores_plot.py index 27c107b456..872e1c28bd 100755 --- a/qiime/quality_scores_plot.py +++ b/qiime/quality_scores_plot.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/qiime/rarefaction.py b/qiime/rarefaction.py index e310ec3baa..fc929bc3a7 100644 --- a/qiime/rarefaction.py +++ b/qiime/rarefaction.py @@ -6,7 +6,7 @@ __credits__ = ["Justin Kuczynski", "Jose Carlos Clemente Litran", "Rob Knight", "Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/relatedness_library.py b/qiime/relatedness_library.py index b88b43820c..bbf611ad95 100644 --- a/qiime/relatedness_library.py +++ b/qiime/relatedness_library.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["William Van Treuren"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Van Treuren" __email__ = "wdwvt1@gmail.com" diff --git a/qiime/remote.py b/qiime/remote.py index 395464e218..c560317f28 100755 --- a/qiime/remote.py +++ b/qiime/remote.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2012, The QIIME project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/qiime/shared_phylotypes.py b/qiime/shared_phylotypes.py index 2a937c6d15..d24af7271d 100644 --- a/qiime/shared_phylotypes.py +++ b/qiime/shared_phylotypes.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jens Reeder, Justin Kuczynski", "Daniel McDonald"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jose Clemente" __email__ = "jose.clemente@gmail.com" diff --git a/qiime/simsam.py b/qiime/simsam.py index 65bc32e7a7..bc7b8e3892 100755 --- a/qiime/simsam.py +++ b/qiime/simsam.py @@ -7,7 +7,7 @@ __credits__ = ["Justin Kuczynski", "Rob Knight", "Jai Ram Rideout", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/sort.py b/qiime/sort.py index cb71ec052d..4911a0abdb 100644 --- a/qiime/sort.py +++ b/qiime/sort.py @@ -13,7 +13,7 @@ __credits__ = ["Greg Caporaso", "Rob Knight", "Daniel McDonald", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/split.py b/qiime/split.py index 7e1808b8ed..de8d1f66a5 100644 --- a/qiime/split.py +++ b/qiime/split.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Daniel McDonald", "Will Van Treuren"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/split_libraries.py b/qiime/split_libraries.py index 3e32f826f7..f0e8496aad 100644 --- a/qiime/split_libraries.py +++ b/qiime/split_libraries.py @@ -30,7 +30,7 @@ "Jesse Stombaugh", "William Walters", "Jens Reeder", "Emily TerAvest", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Walters" __email__ = "rob@spot.colorado.edu, william.a.walters@colorado.edu" diff --git a/qiime/split_libraries_fastq.py b/qiime/split_libraries_fastq.py index 09a713a9c7..5985e10bfa 100644 --- a/qiime/split_libraries_fastq.py +++ b/qiime/split_libraries_fastq.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jose Antonio Navas Molina", "Daniel McDonald"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/split_libraries_lea_seq.py b/qiime/split_libraries_lea_seq.py index 16cd5c9f34..a001d967e3 100644 --- a/qiime/split_libraries_lea_seq.py +++ b/qiime/split_libraries_lea_seq.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2014, The QIIME Project" __credits__ = ["Charudatta Navare", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Charudatta Navare" __email__ = "charudatta.navare@gmail.com" diff --git a/qiime/stats.py b/qiime/stats.py index 37b2cd1ac8..ea96f62a2c 100644 --- a/qiime/stats.py +++ b/qiime/stats.py @@ -8,7 +8,7 @@ "Jose Carlos Clemente Litran", "Greg Caporaso", "Will Van Treuren"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/qiime/summarize_taxa.py b/qiime/summarize_taxa.py index e293aab58e..73a6d2e319 100644 --- a/qiime/summarize_taxa.py +++ b/qiime/summarize_taxa.py @@ -6,7 +6,7 @@ "Rob Knight", "Catherine Lozupone", "Justin Kuczynski", "Julia Goodrich", "Antonio Gonzalez Pena", "Jose Carlos Clemente Litran"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Daniel McDonald" __email__ = "wasade@gmail.com" diff --git a/qiime/supervised_learning.py b/qiime/supervised_learning.py index 40cf97893d..cd585a36e4 100644 --- a/qiime/supervised_learning.py +++ b/qiime/supervised_learning.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Dan Knights", "Luke Ursell", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Dan Knights" __email__ = "danknights@gmail.com" diff --git a/qiime/support_files/R/CSS.r b/qiime/support_files/R/CSS.r new file mode 100644 index 0000000000..af3cca3c7f --- /dev/null +++ b/qiime/support_files/R/CSS.r @@ -0,0 +1,39 @@ +args <- commandArgs(trailingOnly=TRUE) +if(!is.element('--source_dir', args)){ + stop("\n\nPlease use '--source_dir' to specify the R source code directory.\n\n") +} +sourcedir <- args[which(args == '--source_dir') + 1] +source(sprintf('%s/util.r',sourcedir)) + +load.library('optparse') +load.library('metagenomeSeq', bioconductor=TRUE) +load.library('biom') + +# make option list and parse command line +option_list <- list( + make_option(c("--source_dir"), type="character", + help="Path to R source directory [required]."), + make_option(c("-i", "--input_path"), type="character", + help="Input otu table [required]."), + make_option(c("-o", "--out_path"), type="character", default='.', + help="Output directory [default %default]"), + make_option(c("-s", "--output_CSS_statistics"), type="character", default=NULL, + help="output CSS normalization statistics") +) +opts <- parse_args(OptionParser(option_list=option_list), args=args) + +# Error checking +if(is.null(opts$input_path)) stop('Please supply an otu table.') + + +"CSS" <- function(input_path, out_path, output_CSS_statistics=NULL) { + obj = load_biom(input_path) + p = cumNormStatFast(obj) + obj = cumNorm(obj, p = p) + if (!is.null(output_CSS_statistics)) { + exportStats(obj, p=p, file = file.path(output_CSS_statistics)) + } + write_biom(MRexperiment2biom(obj, norm=TRUE, log=TRUE), out_path) + } + +CSS(opts$input_path, opts$out_path, opts$output_CSS_statistics) diff --git a/qiime/support_files/R/DESeq2.r b/qiime/support_files/R/DESeq2.r new file mode 100644 index 0000000000..290b8f65a3 --- /dev/null +++ b/qiime/support_files/R/DESeq2.r @@ -0,0 +1,47 @@ +args <- commandArgs(trailingOnly=TRUE) +if(!is.element('--source_dir', args)){ + stop("\n\nPlease use '--source_dir' to specify the R source code directory.\n\n") +} +sourcedir <- args[which(args == '--source_dir') + 1] +source(sprintf('%s/util.r',sourcedir)) + +load.library('optparse') +load.library('DESeq2', bioconductor=TRUE) +load.library('biom') +load.library('metagenomeSeq', bioconductor=TRUE) + +# make option list and parse command line +option_list <- list( + make_option(c("--source_dir"), type="character", + help="Path to R source directory [required]."), + make_option(c("-i", "--input_path"), type="character", + help="Input otu table [required]."), + make_option(c("-o", "--out_path"), type="character", default='.', + help="Output directory [default %default]"), + make_option(c("-z", "--DESeq_negatives_to_zero"), type="character", default=NULL, + help="set the negatives that result from DESeq transformation to zero") +) +opts <- parse_args(OptionParser(option_list=option_list), args=args) + +# Error checking +if(is.null(opts$input_path)) stop('Please supply an otu table.') + + +"DESeq2"<- function(input_path, out_path, DESeq_negatives_to_zero=NULL, sampleConditions = c(rep("A", floor(ncol(foo)/2)), rep("B", ceiling(ncol(foo)/2)))) { + foo = read_biom(input_path) + x = as(biom_data(foo), "matrix") + # avoid zeros + x = x + 1 + #Create annotated data.frame with mock conditions: these should not influence normalization - just required for DESeqDataSetFromMatrix + sampleTable <- data.frame(sampleName=colnames(x), condition=sampleConditions) + dds <- DESeqDataSetFromMatrix(x, sampleTable, design=~condition) + vsmat = assay(varianceStabilizingTransformation(dds)) + if (!is.null(DESeq_negatives_to_zero)) { + vsmat[vsmat<0]=0 + } + vsmat = newMRexperiment(vsmat) + colnames(vsmat) <- c(colnames(x)) + write_biom(MRexperiment2biom(vsmat), out_path) + } + +DESeq2(opts$input_path, opts$out_path, opts$DESeq_negatives_to_zero) diff --git a/qiime/support_files/R/DESeq2_nbinom.r b/qiime/support_files/R/DESeq2_nbinom.r new file mode 100644 index 0000000000..9d12b9ee15 --- /dev/null +++ b/qiime/support_files/R/DESeq2_nbinom.r @@ -0,0 +1,76 @@ +args <- commandArgs(trailingOnly=TRUE) +if(!is.element('--source_dir', args)){ + stop("\n\nPlease use '--source_dir' to specify the R source code directory.\n\n") +} +sourcedir <- args[which(args == '--source_dir') + 1] +source(sprintf('%s/util.r',sourcedir)) + +load.library('optparse') +load.library('DESeq2', bioconductor=TRUE) +load.library('biom') + +# make option list and parse command line +option_list <- list( + make_option(c("--source_dir"), type="character", + help="Path to R source directory [required]."), + make_option(c("-i", "--input_path"), type="character", + help="Input otu table [required]."), + make_option(c("-c", "--mapping_category"), type="character", + help="Metadata column header giving cluster IDs [required]"), + make_option(c("-x", "--subcategory_1"), type="character", + help="mapping file subcategory_1, e.g. L_palm"), + make_option(c("-y","--subcategory_2"), type="character", + help="mapping file subcategory_2, e.g. Tongue"), + make_option(c("-o", "--out_path"), type="character", default='.', + help="Output directory [default %default]"), + make_option(c("-d", "--DESeq2_diagnostic_plots"), type="character", default=NULL, + help="provide diagnostic plots"), + make_option(c("-e", "--outfile_diagnostic"), type="character", default=NULL, + help="provide outfile of diagnostic plots") +) +opts <- parse_args(OptionParser(option_list=option_list), args=args) + +# Error checking +if(is.null(opts$mapping_category)) stop('Please supply a mapping file header.') +if(is.null(opts$input_path)) stop('Please supply an otu table.') +if(is.null(opts$subcategory_1)) stop('Please supply a subcategory.') +if(is.null(opts$subcategory_2)) stop('Please supply a second subcategory.') + + +"DESeq2_nbinom" <- function(input_path, out_path, mapping_category, subcategory_1, subcategory_2, DESeq2_diagnostic_plots, outfile_diagnostic) { + foo = read_biom(input_path) + x = as(biom_data(foo), "matrix") + # avoid zeros + x = x + 1 + colData <- data.frame(sample_metadata(foo)) + dds <- DESeqDataSetFromMatrix(x, colData, design = as.formula(paste("~",mapping_category))) + suppressWarnings(dds <- try(DESeq(dds, quiet = TRUE), silent = TRUE)) + if (inherits(dds, "try-error")) { + # If the parametric fit failed, try the local. + suppressWarnings(dds <- try(DESeq(dds, fitType = "local", quiet = TRUE), + silent = TRUE)) + if (inherits(dds, "try-error")) { + # If local fails, try the mean + suppressWarnings(dds <- try(DESeq(dds, fitType = "mean", quiet = TRUE), + silent = TRUE)) + } + if (inherits(dds, "try-error")) { + # If still bad, quit with error. + return(NULL) + } + } + res <- results(dds, contrast = c(mapping_category, subcategory_1, subcategory_2)) + resOrdered <- res[order(res$padj),] + df1 <- data.frame(resOrdered) + df1 <- cbind(OTU = rownames(df1), df1) + write.table(df1, out_path, sep="\t", quote=F, row.names=F) + # # #add independent filtering? + if (!is.null(DESeq2_diagnostic_plots)) { + pdf(sprintf("%s", outfile_diagnostic)) + plotMA(res, ylim = c(-3,3)) + plotDispEsts(dds, ylim = c(1e-6, 1e1)) + dev.off() + } + } + +DESeq2_nbinom(opts$input_path, opts$out_path, opts$mapping_category, opts$subcategory_1, opts$subcategory_2, opts$DESeq2_diagnostic_plots, opts$outfile_diagnostic) diff --git a/qiime/support_files/R/fitZIG.r b/qiime/support_files/R/fitZIG.r new file mode 100644 index 0000000000..c5c8cbaa61 --- /dev/null +++ b/qiime/support_files/R/fitZIG.r @@ -0,0 +1,49 @@ +args <- commandArgs(trailingOnly=TRUE) +if(!is.element('--source_dir', args)){ + stop("\n\nPlease use '--source_dir' to specify the R source code directory.\n\n") +} +sourcedir <- args[which(args == '--source_dir') + 1] +source(sprintf('%s/util.r',sourcedir)) + +load.library('optparse') +load.library('metagenomeSeq', bioconductor=TRUE) +load.library('biom') + +# make option list and parse command line +option_list <- list( + make_option(c("--source_dir"), type="character", + help="Path to R source directory [required]."), + make_option(c("-i", "--input_path"), type="character", + help="Input otu table [required]."), + make_option(c("-c", "--mapping_category"), type="character", + help="Metadata column header giving cluster IDs [required]"), + make_option(c("-x", "--subcategory_1"), type="character", + help="mapping file subcategory_1, e.g. Palm"), + make_option(c("-y","--subcategory_2"), type="character", + help="mapping file subcategory_2, e.g. Tongue"), + make_option(c("-o", "--out_path"), type="character", default='.', + help="Output directory [default %default]") +) +opts <- parse_args(OptionParser(option_list=option_list), args=args) + +# Error checking +if(is.null(opts$mapping_category)) stop('Please supply a mapping file header.') +if(is.null(opts$input_path)) stop('Please supply an otu table.') +if(is.null(opts$subcategory_1)) stop('Please supply a subcategory.') +if(is.null(opts$subcategory_2)) stop('Please supply a second subcategory.') + +"fitZIG" <- function(input_path, out_path, mapping_category, subcategory_1, subcategory_2) { + foo = read_biom(input_path) + MGS = biom2MRexperiment(foo) + MGS = cumNorm(MGS,p = cumNormStat(MGS)) + samplesToKeep = which(pData(MGS)[,mapping_category]%in%c(subcategory_1,subcategory_2)) + MGS = MGS[samplesToKeep,] + MGS_category = pData(MGS)[,mapping_category] + ###if continuous or a factor, then error message?? + mod = model.matrix(~MGS_category) + settings = zigControl(maxit=1, verbose=FALSE) + fit = fitZig(obj=MGS, mod=mod, control=settings) + MRfulltable(fit, number = nrow(assayData(MGS)$counts), file=out_path, group=3) + } + +fitZIG(opts$input_path, opts$out_path, opts$mapping_category, opts$subcategory_1, opts$subcategory_2) diff --git a/qiime/support_files/R/util.r b/qiime/support_files/R/util.r index 736b37edc4..7acb152583 100644 --- a/qiime/support_files/R/util.r +++ b/qiime/support_files/R/util.r @@ -4,17 +4,17 @@ # __copyright__ = "Copyright 2011, The QIIME Project" # __credits__ = ["Dan Knights"] # __license__ = "GPL" -# __version__ = "1.8.0-dev" +# __version__ = "1.9.0-rc1" # __maintainer__ = "Dan Knights" # __email__ = "daniel.knights@colorado.edu" -# +# # Attempts to load a given library. If does not exists, fails gracefully # and prints instructions for installing the library -"load.library" <- function(lib.name, quietly=TRUE){ +"load.library" <- function(lib.name, quietly=TRUE, bioconductor=FALSE){ include.custom.library.path() # ensure that custom library is included - + # attempt to load the library, suppress warnings if needed warnings.visible <- get.warning.visibility() if(quietly && warnings.visible) set.warning.visibility(FALSE) @@ -24,18 +24,22 @@ silent=FALSE ) if(quietly && warnings.visible) set.warning.visibility(TRUE) - + + if(bioconductor){ + install.command <- sprintf('source("http://bioconductor.org/biocLite.R"); biocLite("%s")', lib.name) + } else { + install.command <- sprintf('install.packages("%s")', lib.name) + } # if library does not exist or failed, fail gracefully if(class(library.result)=='try-error'){ cat(sprintf('\n\nError encounted loading library %s:\n\n',lib.name),sep='',file=stderr()) cat(library.result[1],'\n\n',sep='',file=stderr()) } else if(!library.result){ help_string1 <- sprintf( - 'To install: open R and run the command "install.packages("%s")".', - lib.name) + 'To install, open R and run the command:\n %s', install.command) cat(sprintf('\n\nLibrary %s not found.\n\n',lib.name),file=stderr()) cat(help_string1,'\n\n',sep='',file=stderr()) - + help_string2 <- sprintf( "If you already have the %s package installed in a local directory, please store the path to that directory in an environment variable @@ -125,5 +129,3 @@ The current R instance knows about these paths: invisible(folds) } } - - diff --git a/qiime/support_files/js/otu_count_display.js b/qiime/support_files/js/otu_count_display.js index 04944c4aa4..91f80f982e 100644 --- a/qiime/support_files/js/otu_count_display.js +++ b/qiime/support_files/js/otu_count_display.js @@ -6,7 +6,7 @@ __author__ = "Jesse Stombaugh" __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jesse Stombaugh"] #remember to add yourself __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Rob Knight" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/qiime/support_files/test_js/test_otu_count_display.html b/qiime/support_files/test_js/test_otu_count_display.html index 145c941fd4..469ce6c71c 100644 --- a/qiime/support_files/test_js/test_otu_count_display.html +++ b/qiime/support_files/test_js/test_otu_count_display.html @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" #consider project name __credits__ = ["Jesse Stombaugh"] #remember to add yourself __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/qiime/test.py b/qiime/test.py index 31f109a41c..e436b48029 100644 --- a/qiime/test.py +++ b/qiime/test.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/transform_coordinate_matrices.py b/qiime/transform_coordinate_matrices.py index 9fcac1896b..7e11d58fb7 100644 --- a/qiime/transform_coordinate_matrices.py +++ b/qiime/transform_coordinate_matrices.py @@ -7,7 +7,7 @@ __credits__ = ["Greg Caporaso", "Justin Kuczynski", "Kyle Patnode", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/tree_compare.py b/qiime/tree_compare.py index 3658eff7b9..7dbf3974fc 100644 --- a/qiime/tree_compare.py +++ b/qiime/tree_compare.py @@ -13,7 +13,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski", "Daniel McDonald"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/trim_sff_primers.py b/qiime/trim_sff_primers.py index f5fb7b2d57..3c8abfa92c 100644 --- a/qiime/trim_sff_primers.py +++ b/qiime/trim_sff_primers.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Rob Knight", 'Kyle Bittinger', "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/qiime/truncate_fasta_qual_files.py b/qiime/truncate_fasta_qual_files.py index 6a724ca258..6e503c6a18 100755 --- a/qiime/truncate_fasta_qual_files.py +++ b/qiime/truncate_fasta_qual_files.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/qiime/truncate_reverse_primer.py b/qiime/truncate_reverse_primer.py index 8ee6210368..0440f470e9 100755 --- a/qiime/truncate_reverse_primer.py +++ b/qiime/truncate_reverse_primer.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters", "Emily TerAvest"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/qiime/util.py b/qiime/util.py index ae6472bdd2..e682000cfe 100644 --- a/qiime/util.py +++ b/qiime/util.py @@ -8,7 +8,7 @@ "Levi McCracken", "Damien Coy", "Yoshiki Vazquez Baeza", "Will Van Treuren", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/validate_demultiplexed_fasta.py b/qiime/validate_demultiplexed_fasta.py index 1793cebd18..52946f2ed2 100755 --- a/qiime/validate_demultiplexed_fasta.py +++ b/qiime/validate_demultiplexed_fasta.py @@ -7,7 +7,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Anton Walters", "Emily TerAvest"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Anton Walters" __email__ = "william.a.walters@gmail.com" diff --git a/qiime/workflow/__init__.py b/qiime/workflow/__init__.py index 294a5091b2..2a272bb3d7 100644 --- a/qiime/workflow/__init__.py +++ b/qiime/workflow/__init__.py @@ -21,6 +21,6 @@ "Daniel McDonald", "Catherine Lozupone"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/workflow/ampliconnoise.py b/qiime/workflow/ampliconnoise.py index a6f0ab41ab..80014a7a2b 100755 --- a/qiime/workflow/ampliconnoise.py +++ b/qiime/workflow/ampliconnoise.py @@ -7,7 +7,7 @@ __credits__ = ["Greg Caporaso", "Kyle Bittinger", "Justin Kuczynski", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/workflow/core_diversity_analyses.py b/qiime/workflow/core_diversity_analyses.py index e9bcb11ce4..edd8c0322c 100644 --- a/qiime/workflow/core_diversity_analyses.py +++ b/qiime/workflow/core_diversity_analyses.py @@ -23,7 +23,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/workflow/downstream.py b/qiime/workflow/downstream.py index 5603b5ebdc..023d7a7d08 100644 --- a/qiime/workflow/downstream.py +++ b/qiime/workflow/downstream.py @@ -8,7 +8,7 @@ "Jesse Stombaugh", "Yoshiki Vazquez Baeza", "Jai Ram Rideout", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/workflow/pick_open_reference_otus.py b/qiime/workflow/pick_open_reference_otus.py index d818787276..423b15efe4 100644 --- a/qiime/workflow/pick_open_reference_otus.py +++ b/qiime/workflow/pick_open_reference_otus.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/workflow/preprocess.py b/qiime/workflow/preprocess.py index dcbffd1c6e..05d09915e4 100644 --- a/qiime/workflow/preprocess.py +++ b/qiime/workflow/preprocess.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/qiime/workflow/upstream.py b/qiime/workflow/upstream.py index e9ef3de881..d6e8c746e7 100644 --- a/qiime/workflow/upstream.py +++ b/qiime/workflow/upstream.py @@ -7,7 +7,7 @@ __credits__ = ["Greg Caporaso", "Kyle Bittinger", "Justin Kuczynski", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/workflow/util.py b/qiime/workflow/util.py index b68d0b36b1..6034835040 100755 --- a/qiime/workflow/util.py +++ b/qiime/workflow/util.py @@ -8,7 +8,7 @@ "Kyle Bittinger", "Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime_test_data/differential_abundance/map.txt b/qiime_test_data/differential_abundance/map.txt new file mode 100644 index 0000000000..7873ced512 --- /dev/null +++ b/qiime_test_data/differential_abundance/map.txt @@ -0,0 +1,11 @@ +#SampleID BarcodeSequence LinkerPrimerSequence Treatment DOB Description +#Example mapping file for the QIIME analysis package. These 9 samples are from a study of the effects of exercise and diet on mouse cardiac physiology (Crawford, et al, PNAS, 2009). +PC.354 AGCACGAGCCTA YATGCTGCCTCCCGTAGGAGT Control 20061218 Control_mouse_I.D._354 +PC.355 AACTCGTCGATG YATGCTGCCTCCCGTAGGAGT Control 20061218 Control_mouse_I.D._355 +PC.356 ACAGACCACTCA YATGCTGCCTCCCGTAGGAGT Control 20061126 Control_mouse_I.D._356 +PC.481 ACCAGCGACTAG YATGCTGCCTCCCGTAGGAGT Control 20070314 Control_mouse_I.D._481 +PC.593 AGCAGCACTTGT YATGCTGCCTCCCGTAGGAGT Control 20071210 Control_mouse_I.D._593 +PC.607 AACTGTGCGTAC YATGCTGCCTCCCGTAGGAGT Fast 20071112 Fasting_mouse_I.D._607 +PC.634 ACAGAGTCGGCT YATGCTGCCTCCCGTAGGAGT Fast 20080116 Fasting_mouse_I.D._634 +PC.635 ACCGCAGAGTCA YATGCTGCCTCCCGTAGGAGT Fast 20080116 Fasting_mouse_I.D._635 +PC.636 ACGGTGAGTGTC YATGCTGCCTCCCGTAGGAGT Fast 20080116 Fasting_mouse_I.D._636 diff --git a/qiime_test_data/differential_abundance/otu_table.biom b/qiime_test_data/differential_abundance/otu_table.biom new file mode 100644 index 0000000000..51f508ffe5 --- /dev/null +++ b/qiime_test_data/differential_abundance/otu_table.biom @@ -0,0 +1 @@ +{"rows": [{"id": "0", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Bacillales", "f__Staphylococcaceae"]}}, {"id": "1", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "2", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "3", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "4", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "5", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "6", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "7", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "8", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "9", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "10", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "11", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "12", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "13", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "14", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Ruminococcaceae"]}}, {"id": "15", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Lactobacillales", "f__Streptococcaceae"]}}, {"id": "16", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "17", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Actinobacteria", "c__Actinobacteria", "o__Coriobacteriales", "f__Coriobacteriaceae"]}}, {"id": "18", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Actinobacteria", "c__Actinobacteria", "o__Coriobacteriales", "f__Coriobacteriaceae"]}}, {"id": "19", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "20", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Porphyromonadaceae"]}}, {"id": "21", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Ruminococcaceae"]}}, {"id": "22", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "23", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Ruminococcaceae"]}}, {"id": "24", "metadata": {"taxonomy": ["Root", "k__Bacteria"]}}, {"id": "25", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "26", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Ruminococcaceae"]}}, {"id": "27", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "28", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "29", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "30", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales"]}}, {"id": "31", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__TM7", "c__TM7-3", "o__CW040", "f__F16"]}}, {"id": "32", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "33", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "34", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Ruminococcaceae"]}}, {"id": "35", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Actinobacteria", "c__Actinobacteria", "o__Coriobacteriales", "f__Coriobacteriaceae"]}}, {"id": "36", "metadata": {"taxonomy": ["Root", "k__Bacteria"]}}, {"id": "37", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "38", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Tenericutes", "c__Erysipelotrichi", "o__Erysipelotrichales", "f__Erysipelotrichaceae"]}}, {"id": "39", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Actinobacteria", "c__Actinobacteria", "o__Coriobacteriales", "f__Coriobacteriaceae"]}}, {"id": "40", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "41", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "42", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "43", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "44", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Ruminococcaceae"]}}, {"id": "45", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "46", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Deferribacteres", "c__Deferribacteres", "o__Deferribacterales", "f__Deferribacteraceae"]}}, {"id": "47", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "48", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "49", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "50", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "51", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "52", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "53", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "54", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "55", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Lactobacillales", "f__Lactobacillaceae"]}}, {"id": "56", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "57", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Bacteroidaceae"]}}, {"id": "58", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "59", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "60", "metadata": {"taxonomy": ["Root", "k__Bacteria"]}}, {"id": "61", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "62", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "63", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "64", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "65", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales"]}}, {"id": "66", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "67", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "68", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "69", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Bacteroidaceae"]}}, {"id": "70", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Ruminococcaceae"]}}, {"id": "71", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__"]}}, {"id": "72", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "73", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Proteobacteria", "c__Deltaproteobacteria", "o__Desulfovibrionales", "f__Desulfovibrionaceae"]}}, {"id": "74", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "75", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "76", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Tenericutes", "c__Erysipelotrichi", "o__Erysipelotrichales", "f__Erysipelotrichaceae"]}}, {"id": "77", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "78", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Tenericutes", "c__Erysipelotrichi", "o__Erysipelotrichales", "f__Erysipelotrichaceae"]}}, {"id": "79", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "80", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "81", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "82", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Bacteroidaceae"]}}, {"id": "83", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Ruminococcaceae"]}}, {"id": "84", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "85", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "86", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "87", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "88", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "89", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "90", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "91", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Tenericutes", "c__Mollicutes", "o__RF39", "f__"]}}, {"id": "92", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "93", "metadata": {"taxonomy": ["Root", 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[386, 2, 1.0], [387, 1, 1.0], [387, 2, 1.0], [388, 2, 1.0], [389, 2, 1.0], [390, 2, 1.0], [391, 8, 1.0], [392, 2, 2.0], [392, 5, 2.0], [392, 6, 20.0], [392, 8, 3.0], [393, 0, 1.0], [393, 2, 1.0], [394, 2, 1.0], [395, 3, 1.0], [396, 2, 1.0], [396, 6, 2.0], [397, 0, 3.0], [397, 1, 1.0], [397, 2, 2.0], [397, 5, 9.0], [397, 6, 1.0], [397, 7, 1.0], [397, 8, 1.0], [398, 7, 1.0], [399, 8, 2.0], [400, 0, 4.0], [400, 2, 3.0], [400, 3, 1.0], [400, 5, 4.0], [400, 6, 2.0], [400, 8, 5.0], [401, 8, 1.0], [402, 6, 1.0], [403, 4, 1.0], [404, 6, 1.0], [405, 3, 1.0], [406, 0, 1.0], [406, 1, 1.0], [406, 2, 1.0], [406, 3, 2.0], [406, 6, 2.0], [406, 8, 1.0], [407, 8, 1.0], [408, 8, 4.0], [409, 0, 1.0], [410, 3, 9.0], [410, 8, 3.0], [411, 0, 1.0], [411, 6, 1.0], [412, 7, 1.0], [413, 0, 1.0], [414, 0, 2.0], [414, 1, 10.0], [414, 8, 8.0], [415, 6, 1.0], [416, 2, 1.0], [416, 3, 3.0], [417, 6, 1.0], [418, 0, 1.0]], "columns": [{"id": "PC.636", "metadata": null}, {"id": "PC.635", "metadata": null}, {"id": "PC.356", "metadata": null}, {"id": "PC.481", "metadata": null}, {"id": "PC.354", "metadata": null}, {"id": "PC.593", "metadata": null}, {"id": "PC.355", "metadata": null}, {"id": "PC.607", "metadata": null}, {"id": "PC.634", "metadata": null}], "generated_by": "QIIME 1.4.0-dev, svn revision 2728", "matrix_type": "sparse", "shape": [419, 9], "format_url": "http://www.qiime.org/svn_documentation/documentation/biom_format.html", "date": "2012-02-07T06:12:49.215476", "type": "OTU table", "id": null, "matrix_element_type": "float"} \ No newline at end of file diff --git a/scripts/add_alpha_to_mapping_file.py b/scripts/add_alpha_to_mapping_file.py index a2dfa98db5..98fe051256 100755 --- a/scripts/add_alpha_to_mapping_file.py +++ b/scripts/add_alpha_to_mapping_file.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Yoshiki Vazquez-Baeza", "Antonio Gonzalez-Pena"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Yoshiki Vazquez-Baeza" __email__ = "yoshiki89@gmail.com" diff --git a/scripts/add_qiime_labels.py b/scripts/add_qiime_labels.py index 10aac82637..82838b24fb 100755 --- a/scripts/add_qiime_labels.py +++ b/scripts/add_qiime_labels.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/scripts/adjust_seq_orientation.py b/scripts/adjust_seq_orientation.py index f584c47efe..8f53912b49 100755 --- a/scripts/adjust_seq_orientation.py +++ b/scripts/adjust_seq_orientation.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Antonio Gonzalez Pena"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Antonio Gonzalez Pena" __email__ = "antgonza@gmail.com" diff --git a/scripts/align_seqs.py b/scripts/align_seqs.py index 93beba176c..4b9c8b2c22 100755 --- a/scripts/align_seqs.py +++ b/scripts/align_seqs.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/alpha_diversity.py b/scripts/alpha_diversity.py index 639cf571a3..4a4fb43df8 100755 --- a/scripts/alpha_diversity.py +++ b/scripts/alpha_diversity.py @@ -7,7 +7,7 @@ __credits__ = ["Justin Kuczynski", "Rob Knight", "Jose Antonio Navas Molina", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/alpha_rarefaction.py b/scripts/alpha_rarefaction.py index 81c692a9c6..4f50001b8e 100755 --- a/scripts/alpha_rarefaction.py +++ b/scripts/alpha_rarefaction.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/ampliconnoise.py b/scripts/ampliconnoise.py index 0477c667c5..705e9f159a 100755 --- a/scripts/ampliconnoise.py +++ b/scripts/ampliconnoise.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski", "Jose A. Navas Molina"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/assign_taxonomy.py b/scripts/assign_taxonomy.py index 51b361699d..ec1751ef9b 100755 --- a/scripts/assign_taxonomy.py +++ b/scripts/assign_taxonomy.py @@ -7,7 +7,7 @@ __credits__ = ["Rob Knight", "Greg Caporaso", "Kyle Bittinger", "Antonio Gonzalez Pena", "David Soergel", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Antonio Gonzalez Pena" __email__ = "antgonza@gmail.com" diff --git a/scripts/beta_diversity.py b/scripts/beta_diversity.py index eb48474ec8..5fcb6b2a9c 100755 --- a/scripts/beta_diversity.py +++ b/scripts/beta_diversity.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski", "Rob Knight", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/beta_diversity_through_plots.py b/scripts/beta_diversity_through_plots.py index 831d7251e9..3bb0e2306e 100755 --- a/scripts/beta_diversity_through_plots.py +++ b/scripts/beta_diversity_through_plots.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Kestrel Gorlick"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/beta_significance.py b/scripts/beta_significance.py index f42a92c58b..df41d58250 100755 --- a/scripts/beta_significance.py +++ b/scripts/beta_significance.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski", "Jose Antonio Navas", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/blast_wrapper.py b/scripts/blast_wrapper.py index 51e5271b38..f631128565 100755 --- a/scripts/blast_wrapper.py +++ b/scripts/blast_wrapper.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jesse Stombaugh"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/categorized_dist_scatterplot.py b/scripts/categorized_dist_scatterplot.py index 2a1fe93fac..9ef0838362 100755 --- a/scripts/categorized_dist_scatterplot.py +++ b/scripts/categorized_dist_scatterplot.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/check_id_map.py b/scripts/check_id_map.py index 2aecb3004d..885b49533c 100755 --- a/scripts/check_id_map.py +++ b/scripts/check_id_map.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters", "Luke Ursell"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/scripts/clean_raxml_parsimony_tree.py b/scripts/clean_raxml_parsimony_tree.py index 8f4feaf2c3..49486e177e 100755 --- a/scripts/clean_raxml_parsimony_tree.py +++ b/scripts/clean_raxml_parsimony_tree.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Jesse Stombaugh"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/scripts/cluster_quality.py b/scripts/cluster_quality.py index c7037207e6..d7ca38cf63 100755 --- a/scripts/cluster_quality.py +++ b/scripts/cluster_quality.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/collapse_samples.py b/scripts/collapse_samples.py index 82bb64787f..dfdaffddc8 100755 --- a/scripts/collapse_samples.py +++ b/scripts/collapse_samples.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2014, The QIIME Project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/collate_alpha.py b/scripts/collate_alpha.py index 64af745b8d..572b47a646 100755 --- a/scripts/collate_alpha.py +++ b/scripts/collate_alpha.py @@ -15,7 +15,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/compare_alpha_diversity.py b/scripts/compare_alpha_diversity.py index e01aaea0a6..54c2dd007e 100755 --- a/scripts/compare_alpha_diversity.py +++ b/scripts/compare_alpha_diversity.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["William Van Treuren", "Greg Caparaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Van Treuren" __email__ = "vantreur@colorado.edu" diff --git a/scripts/compare_categories.py b/scripts/compare_categories.py index 3ee3d49b3d..1d21198ccc 100755 --- a/scripts/compare_categories.py +++ b/scripts/compare_categories.py @@ -6,7 +6,7 @@ __credits__ = ["Logan Knecht", "Michael Dwan", "Damien Coy", "Jai Ram Rideout", "Levi McCracken"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/scripts/compare_distance_matrices.py b/scripts/compare_distance_matrices.py index ca387b2884..38e7b9a32a 100755 --- a/scripts/compare_distance_matrices.py +++ b/scripts/compare_distance_matrices.py @@ -6,7 +6,7 @@ __credits__ = ["Jai Ram Rideout", "Michael Dwan", "Logan Knecht", "Damien Coy", "Levi McCracken", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/scripts/compare_taxa_summaries.py b/scripts/compare_taxa_summaries.py index 8bc5fefc35..739335ad57 100755 --- a/scripts/compare_taxa_summaries.py +++ b/scripts/compare_taxa_summaries.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2012, The QIIME project" __credits__ = ["Jai Ram Rideout", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/scripts/compare_trajectories.py b/scripts/compare_trajectories.py index 054b857970..b08ceddd40 100755 --- a/scripts/compare_trajectories.py +++ b/scripts/compare_trajectories.py @@ -6,7 +6,7 @@ __credits__ = ["Jose Antonio Navas Molina", "Antonio Gonzalez Pena", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jose Antonio Navas Molina" __email__ = "josenavasmolina@gmail.com" diff --git a/scripts/compute_core_microbiome.py b/scripts/compute_core_microbiome.py index afe1369377..fb5c4583da 100755 --- a/scripts/compute_core_microbiome.py +++ b/scripts/compute_core_microbiome.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/compute_taxonomy_ratios.py b/scripts/compute_taxonomy_ratios.py index 3f2fe6b077..16fb454369 100755 --- a/scripts/compute_taxonomy_ratios.py +++ b/scripts/compute_taxonomy_ratios.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2014, The QIIME project" __credits__ = ["Daniel McDonald", "Greg Caporaso", "Jai Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Daniel McDonald" __email__ = "mcdonadt@colorado.edu" diff --git a/scripts/conditional_uncovered_probability.py b/scripts/conditional_uncovered_probability.py index e82e150291..7f459572da 100755 --- a/scripts/conditional_uncovered_probability.py +++ b/scripts/conditional_uncovered_probability.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jens Reeder", "Jose Antonio Navas Molina", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" __status__ = "Development" diff --git a/scripts/consensus_tree.py b/scripts/consensus_tree.py index 6225973f26..2c2525e263 100755 --- a/scripts/consensus_tree.py +++ b/scripts/consensus_tree.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "justinak@gmail.com" diff --git a/scripts/convert_fastaqual_fastq.py b/scripts/convert_fastaqual_fastq.py index 0f00ea59c4..5bcfe01772 100755 --- a/scripts/convert_fastaqual_fastq.py +++ b/scripts/convert_fastaqual_fastq.py @@ -5,7 +5,7 @@ __credits__ = ["Adam Robbins-Pianka, Abhisaar Yadav", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Adam Robbins-Pianka" __email__ = "adam.robbinspianka@colorado.edu" diff --git a/scripts/convert_unifrac_sample_mapping_to_otu_table.py b/scripts/convert_unifrac_sample_mapping_to_otu_table.py index facae5b4e0..fc9b58770b 100755 --- a/scripts/convert_unifrac_sample_mapping_to_otu_table.py +++ b/scripts/convert_unifrac_sample_mapping_to_otu_table.py @@ -5,7 +5,7 @@ __credits__ = ["Catherine Lozupone", "Greg Caporaso", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Cathy Lozupone" __email__ = "lozupone@colorado.edu" diff --git a/scripts/core_diversity_analyses.py b/scripts/core_diversity_analyses.py index 020bebd929..bc4fabd39d 100755 --- a/scripts/core_diversity_analyses.py +++ b/scripts/core_diversity_analyses.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/count_seqs.py b/scripts/count_seqs.py index d0a765c85f..f54cac6144 100755 --- a/scripts/count_seqs.py +++ b/scripts/count_seqs.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/demultiplex_fasta.py b/scripts/demultiplex_fasta.py index ac55b02e85..05f59fc9e9 100755 --- a/scripts/demultiplex_fasta.py +++ b/scripts/demultiplex_fasta.py @@ -13,7 +13,7 @@ "Jens Reeder", "Jose Antonio Navas Molina"] # remember to add yourself __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Walters" __email__ = "william.a.walters@colorado.edu" diff --git a/scripts/denoise_wrapper.py b/scripts/denoise_wrapper.py index b7ba8cd6d1..0da4550be1 100755 --- a/scripts/denoise_wrapper.py +++ b/scripts/denoise_wrapper.py @@ -8,7 +8,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jens Reeder", "Greg Caporaso", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/scripts/denoiser.py b/scripts/denoiser.py index fea2a51a29..88f4380c76 100755 --- a/scripts/denoiser.py +++ b/scripts/denoiser.py @@ -8,7 +8,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/scripts/denoiser_preprocess.py b/scripts/denoiser_preprocess.py index 877c085a0f..a3ba2c38a8 100755 --- a/scripts/denoiser_preprocess.py +++ b/scripts/denoiser_preprocess.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/scripts/denoiser_worker.py b/scripts/denoiser_worker.py index 56dfe4471c..5e7ed953e5 100755 --- a/scripts/denoiser_worker.py +++ b/scripts/denoiser_worker.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/scripts/detrend.py b/scripts/detrend.py index e1d3427307..ef00e4f1f7 100755 --- a/scripts/detrend.py +++ b/scripts/detrend.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2012, The QIIME Project" __credits__ = ["Dan Knights"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Dan Knights" __email__ = "danknights@gmail.com" diff --git a/scripts/differential_abundance.py b/scripts/differential_abundance.py new file mode 100755 index 0000000000..8cb2b1cc8d --- /dev/null +++ b/scripts/differential_abundance.py @@ -0,0 +1,136 @@ +#!/usr/bin/env python +# File created on 14 Jul 2014 +from __future__ import division + +from qiime.util import parse_command_line_parameters, make_option +from qiime.differential_abundance import (DA_fitZIG, multiple_file_DA_fitZIG, + DA_DESeq2, multiple_file_DA_DESeq2, algorithm_list) + +import os + +__author__ = "Sophie Weiss" +__copyright__ = "Copyright 2014, The QIIME Project" +__credits__ = ["Sophie Weiss"] +__license__ = "GPL" +__version__ = "1.9.0-rc1" +__maintainer__ = "Sophie Weiss" +__email__ = "sophie.sjw@gmail.com" + +script_info = {} +script_info['brief_description'] = "Identify OTUs that are differentially abundance across two sample categories" +script_info['script_description'] = \ +"""OTU differential abundance testing is commonly used to identify OTUs that +differ between two mapping file sample categories (i.e. Palm and Tongue body +sites). These methods can be used in comparison to group_significance.py on a +rarefied matrix, and we would always recommend comparing the results of these +approaches to the rarefied/group_significance.py approaches. We would also +recommend treating the differentially abundant OTUs identified by these (fitZIG +and DESeq negative binomial) techinques with caution, as they assume a +distribution and are therefore parametric. They are also newer techinques that +are less well tested compared to rarefying/group_signficance.py. The input is +a raw (not rarefied) matrix having uneven column sums. With these techniques, +we would still recommend removing low depth samples (e.g. below 1000 sequences +per sample) from the data set. The DESeq2 method should NOT be used if the fit +line on the disperison plot (one of the diagnostic plots output by the -d, or +--DESeq2_diagnostic_plots option) does not look smooth and there are big gaps +in the points. DESeq2 is stronger at very small/smaller data sets and the +run-time beyond 100 total samples becomes very long. fitZIG is a better +algorithm for over 100 samples per category (e.g. Palm samples). In simulation, +these techinques have higher sensitivity, but sometimes higher false positive +rate compared to group_significance.py, especially with low and very uneven +library sizes. In practice and with real data, we do not observe much of a +difference between these results and group_significance.py. For more on these +techinques please see Paulson, JN, et al. 'Differential abundance analysis for +microbial marker-gene surveys.' Nature Methods 2013. For DESeq2/DESeq please +see Love, MI et al. 'Moderated estimation of fold change and dispersion for +RNA-Seq data with DESeq2,' Genome Biology 2014. Anders S, Huber W. +'Differential expression analysis for sequence count data.' Genome Biology 2010. +Additionally, you can also read the vignettes for each of the techinques on the +Bioconductor/R websites.""" +script_info['script_usage'] = [] +script_info['script_usage'].append(( + "OTU Differential Abundance Testing with metagenomeSeq_fitZIG", + """Apply metagenomeSeq_fitZIG differential OTU abundance testing to a """ + """raw (NOT normalized) BIOM table to test for differences in OTU """ + """abundance between samples in the Treatment:Control and """ + """Treatment:Fast groups.""", + "%prog -i otu_table.biom -o diff_otus.txt -m map.txt -a metagenomeSeq_fitZIG -c Treatment -x Control -y Fast") + ) +script_info['script_usage'].append(( + "OTU Differential Abundance Testing with DESeq2_nbinom", + """Apply DESeq2_nbinom differential OTU abundance testing to a """ + """raw (NOT normalized) BIOM table to test for differences in OTU """ + """abundance between samples in the Treatment:Control and """ + """Treatment:Fast groups, including output of plots.""", + "%prog -i otu_table.biom -o diff_otus.txt -m map.txt -a DESeq2_nbinom -c Treatment -x Control -y Fast -d") + ) +script_info['output_description']= "The resulting output OTU txt file contains a list of all the OTUs in the input matrix, along with their associated statistics and FDR p-values." +script_info['required_options']=[ +] +script_info['optional_options']=[ + make_option('-i', '--input_path', type='existing_path', + help='path to the input BIOM file (e.g., the output ' + 'from OTU picking) or directory containing input BIOM files ' + 'for batch processing [REQUIRED if not passing -l]'), + make_option('-o', '--out_path', type='new_path', + help='output filename for single file operation, or output ' + 'directory for batch processing [REQUIRED if not passing -l]'), +make_option('-a', '--algorithm', default='metagenomeSeq_fitZIG', type='choice', + choices=algorithm_list(), help='differential abundance algorithm to ' + 'apply to input BIOM table(s) [default: %default]' + ' Available options are: ' + '%s' % ', '.join(algorithm_list())), +make_option('-m', '--mapping_file_path', type='existing_filepath', + help='path to mapping file [REQUIRED if not passing -l]'), +make_option('-c', '--mapping_file_category', + help='mapping file category [REQUIRED if not passing -l]'), +make_option('-x', '--mapping_file_subcategory_1', + help='mapping file subcategory [REQUIRED if not passing -l]'), +make_option('-y', '--mapping_file_subcategory_2', + help='mapping file subcategory [REQUIRED if not passing -l]'), +make_option('-l', '--list_algorithms', action='store_true', default=False, + help='show available differential abundance algorithms and exit ' + '[default: %default]'), +make_option('-d', '--DESeq2_diagnostic_plots', default=False, + action='store_true', help='show a MA plot - y axis: log2 fold change, ' + 'x axis: average size factor normalized OTU value. Also show a Dispersion ' + 'Estimate plot - visualize the fitted dispersion vs. mean relationship ' + '[default: %default]'), + ] +script_info['version'] = __version__ + +def main(): + option_parser, opts, args = parse_command_line_parameters(**script_info) + input_path = opts.input_path + out_path = opts.out_path + algorithm = opts.algorithm + mapping_fp = opts.mapping_file_path + mapping_category = opts.mapping_file_category + subcategory_1 = opts.mapping_file_subcategory_1 + subcategory_2 = opts.mapping_file_subcategory_2 + list_algorithms = opts.list_algorithms + DESeq2_diagnostic_plots = opts.DESeq2_diagnostic_plots + + if list_algorithms: + print 'Available differential abundance algorithms are:\n%s' % ', '.join(algorithm_list()) + elif algorithm == 'metagenomeSeq_fitZIG': + if os.path.isdir(input_path): + multiple_file_DA_fitZIG(input_path, out_path, mapping_fp, mapping_category, subcategory_1, subcategory_2) + elif os.path.isfile(input_path): + DA_fitZIG(input_path, out_path, mapping_fp, mapping_category, subcategory_1, subcategory_2) + else: + # it shouldn't be possible to get here + option_parser.error("Unknown input type: %s" % input_path) + elif algorithm == 'DESeq2_nbinom': + if os.path.isdir(input_path): + multiple_file_DA_DESeq2(input_path, out_path, mapping_fp, mapping_category, subcategory_1, subcategory_2, DESeq2_diagnostic_plots) + elif os.path.isfile(input_path): + DA_DESeq2(input_path, out_path, mapping_fp, mapping_category, subcategory_1, subcategory_2, DESeq2_diagnostic_plots) + else: + # it shouldn't be possible to get here + option_parser.error("Unknown input type: %s" % input_path) + else: + # it shouldn't be possible to get here + option_parser.error("Unknown normalization algorithm: %s" % algorithm) + +if __name__ == "__main__": + main() diff --git a/scripts/dissimilarity_mtx_stats.py b/scripts/dissimilarity_mtx_stats.py index ae271877ed..c8ac0934b3 100755 --- a/scripts/dissimilarity_mtx_stats.py +++ b/scripts/dissimilarity_mtx_stats.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/distance_matrix_from_mapping.py b/scripts/distance_matrix_from_mapping.py index 69a359ef6f..0531909b5c 100755 --- a/scripts/distance_matrix_from_mapping.py +++ b/scripts/distance_matrix_from_mapping.py @@ -7,7 +7,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Antonio Gonzalez Pena", "Andrew J. King"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Antonio Gonzalez Pena" __email__ = "antgonza@gmail.com" diff --git a/scripts/estimate_observation_richness.py b/scripts/estimate_observation_richness.py index 50049ca6e1..08418e8e61 100755 --- a/scripts/estimate_observation_richness.py +++ b/scripts/estimate_observation_richness.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2013, The QIIME Project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/scripts/exclude_seqs_by_blast.py b/scripts/exclude_seqs_by_blast.py index 4b19616af1..aea654f94a 100755 --- a/scripts/exclude_seqs_by_blast.py +++ b/scripts/exclude_seqs_by_blast.py @@ -26,7 +26,7 @@ "Jose Antonio Navas Molina", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jesse Zaneveld" __email__ = "zaneveld@gmail.com" diff --git a/scripts/extract_barcodes.py b/scripts/extract_barcodes.py index c8b65013b2..2c20de7786 100755 --- a/scripts/extract_barcodes.py +++ b/scripts/extract_barcodes.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Walters" __email__ = "william.a.walters@gmail.com" diff --git a/scripts/extract_reads_from_interleaved_file.py b/scripts/extract_reads_from_interleaved_file.py index 86cc57d7ee..5f3ef0d3fb 100755 --- a/scripts/extract_reads_from_interleaved_file.py +++ b/scripts/extract_reads_from_interleaved_file.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2013, The QIIME Project" __credits__ = ["Antonio Gonzalez Pena"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Antonio Gonzalez Pena" __email__ = "antgonza@gmail.com" diff --git a/scripts/extract_seqs_by_sample_id.py b/scripts/extract_seqs_by_sample_id.py index 41b569e198..85f3a93359 100755 --- a/scripts/extract_seqs_by_sample_id.py +++ b/scripts/extract_seqs_by_sample_id.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/filter_alignment.py b/scripts/filter_alignment.py index b2637ea6cd..70951b65e6 100755 --- a/scripts/filter_alignment.py +++ b/scripts/filter_alignment.py @@ -7,7 +7,7 @@ __credits__ = ["Greg Caporaso", "Justin Kuczynski", "Dan Knights", "Doug Wendel", "William Walters", "John Chase"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/filter_distance_matrix.py b/scripts/filter_distance_matrix.py index 9249f1eae5..4bc0a47e8c 100755 --- a/scripts/filter_distance_matrix.py +++ b/scripts/filter_distance_matrix.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2010, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/filter_fasta.py b/scripts/filter_fasta.py index 23709989b2..c68e2dd698 100755 --- a/scripts/filter_fasta.py +++ b/scripts/filter_fasta.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jens Reeder", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/filter_otus_by_sample.py b/scripts/filter_otus_by_sample.py index 93993e7209..dfb266ce26 100755 --- a/scripts/filter_otus_by_sample.py +++ b/scripts/filter_otus_by_sample.py @@ -8,7 +8,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jesse Stombaugh"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/scripts/filter_otus_from_otu_table.py b/scripts/filter_otus_from_otu_table.py index acef4d2811..c729ecbd97 100755 --- a/scripts/filter_otus_from_otu_table.py +++ b/scripts/filter_otus_from_otu_table.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/filter_samples_from_otu_table.py b/scripts/filter_samples_from_otu_table.py index 9428b708b4..cc0f1829c1 100755 --- a/scripts/filter_samples_from_otu_table.py +++ b/scripts/filter_samples_from_otu_table.py @@ -11,7 +11,7 @@ "Daniel McDonald", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/filter_taxa_from_otu_table.py b/scripts/filter_taxa_from_otu_table.py index ad66729f9d..9a5535a4e1 100755 --- a/scripts/filter_taxa_from_otu_table.py +++ b/scripts/filter_taxa_from_otu_table.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/filter_tree.py b/scripts/filter_tree.py index ee881f4029..a27e174fbf 100755 --- a/scripts/filter_tree.py +++ b/scripts/filter_tree.py @@ -10,7 +10,7 @@ "Daniel McDonald", "Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Van Treuren" __email__ = "vantreur@colorado.edu" diff --git a/scripts/fix_arb_fasta.py b/scripts/fix_arb_fasta.py index b20da825f7..99f012cfc0 100755 --- a/scripts/fix_arb_fasta.py +++ b/scripts/fix_arb_fasta.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Rob Knight", "Daniel McDonald", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/group_significance.py b/scripts/group_significance.py index 0fe49d8c3b..b70104287c 100755 --- a/scripts/group_significance.py +++ b/scripts/group_significance.py @@ -9,7 +9,7 @@ "Jesse Stombaugh", "Doug Wendel", "Dan Knights", "Greg Caporaso", "Jai Ram Rideout", "Daniel McDonald"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Will Van Treuren" __email__ = "wdwvt1@gmail.com" diff --git a/scripts/identify_chimeric_seqs.py b/scripts/identify_chimeric_seqs.py index 62d92fb41f..14335e956b 100755 --- a/scripts/identify_chimeric_seqs.py +++ b/scripts/identify_chimeric_seqs.py @@ -12,7 +12,7 @@ "Jens Reeder", "William Walters"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/identify_missing_files.py b/scripts/identify_missing_files.py index 4c339890cc..a784966b10 100755 --- a/scripts/identify_missing_files.py +++ b/scripts/identify_missing_files.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/identify_paired_differences.py b/scripts/identify_paired_differences.py index 3ce8eb8b3c..8b3e83b269 100755 --- a/scripts/identify_paired_differences.py +++ b/scripts/identify_paired_differences.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2013, The QIIME project" __credits__ = ["Greg Caporaso", "Jose Carlos Clemente Litran"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/inflate_denoiser_output.py b/scripts/inflate_denoiser_output.py index ce948fa764..ab25d4b4e1 100755 --- a/scripts/inflate_denoiser_output.py +++ b/scripts/inflate_denoiser_output.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/jackknifed_beta_diversity.py b/scripts/jackknifed_beta_diversity.py index ab695a9900..1db6e94623 100755 --- a/scripts/jackknifed_beta_diversity.py +++ b/scripts/jackknifed_beta_diversity.py @@ -9,7 +9,7 @@ "Justin Kuczynski", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/join_paired_ends.py b/scripts/join_paired_ends.py index f9ac82c2dd..62dd303683 100755 --- a/scripts/join_paired_ends.py +++ b/scripts/join_paired_ends.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2013, The QIIME Project" __credits__ = ["Mike Robeson"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Mike Robeson" __email__ = "robesonms@ornl.gov" diff --git a/scripts/load_remote_mapping_file.py b/scripts/load_remote_mapping_file.py index 6b6fb3a88f..229f3b8469 100755 --- a/scripts/load_remote_mapping_file.py +++ b/scripts/load_remote_mapping_file.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2012, The QIIME project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/scripts/make_2d_plots.py b/scripts/make_2d_plots.py index 526e4ced62..ee3ae9f900 100755 --- a/scripts/make_2d_plots.py +++ b/scripts/make_2d_plots.py @@ -8,7 +8,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jesse Stombaugh", "Jose Antonio Navas Molina", "John Chase"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/scripts/make_bipartite_network.py b/scripts/make_bipartite_network.py index 9e0603a9d4..2368cfdbae 100755 --- a/scripts/make_bipartite_network.py +++ b/scripts/make_bipartite_network.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2013, The QIIME project" __credits__ = ["Will Van Treuren, Julia Goodrich, Luke Ursell"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Will Van Treuren" __email__ = "wdwvt1@gmail.com" diff --git a/scripts/make_bootstrapped_tree.py b/scripts/make_bootstrapped_tree.py index 9c150ff706..4027143b67 100755 --- a/scripts/make_bootstrapped_tree.py +++ b/scripts/make_bootstrapped_tree.py @@ -9,7 +9,7 @@ "Jesse Stombaugh", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/make_distance_boxplots.py b/scripts/make_distance_boxplots.py index d710671f77..3f7f055a32 100755 --- a/scripts/make_distance_boxplots.py +++ b/scripts/make_distance_boxplots.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/scripts/make_distance_comparison_plots.py b/scripts/make_distance_comparison_plots.py index 581b63b52f..20b54587ea 100755 --- a/scripts/make_distance_comparison_plots.py +++ b/scripts/make_distance_comparison_plots.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/scripts/make_fastq.py b/scripts/make_fastq.py index 466dc947e7..ae49309899 100755 --- a/scripts/make_fastq.py +++ b/scripts/make_fastq.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Rob Knight", "Jens Reeder"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/scripts/make_library_id_lists.py b/scripts/make_library_id_lists.py index dbd8ac3adb..7d4fb2034c 100755 --- a/scripts/make_library_id_lists.py +++ b/scripts/make_library_id_lists.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Rob Knight", "Doug Wendel"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/scripts/make_otu_heatmap.py b/scripts/make_otu_heatmap.py index f6947b259f..52a451ccef 100755 --- a/scripts/make_otu_heatmap.py +++ b/scripts/make_otu_heatmap.py @@ -10,7 +10,7 @@ "Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Dan Knights" __email__ = "daniel.knights@colorado.edu" diff --git a/scripts/make_otu_network.py b/scripts/make_otu_network.py index b654b2cb71..137eca37f0 100755 --- a/scripts/make_otu_network.py +++ b/scripts/make_otu_network.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Julia Goodrich", "Jose Carlos Clemente Litran"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jose Clemente" __email__ = "jose.clemente@gmail.com" diff --git a/scripts/make_otu_table.py b/scripts/make_otu_table.py index dabf54fdb7..68121f9872 100755 --- a/scripts/make_otu_table.py +++ b/scripts/make_otu_table.py @@ -12,7 +12,7 @@ "Adam Robbins-Pianka", "Sami Pietila"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/make_per_library_sff.py b/scripts/make_per_library_sff.py index 8b70f687d6..4257a1dddf 100755 --- a/scripts/make_per_library_sff.py +++ b/scripts/make_per_library_sff.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Rob Knight", "Daniel McDonald", "Kyle Bittinger"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/scripts/make_phylogeny.py b/scripts/make_phylogeny.py index 9e5ce410b0..28c438b4f9 100755 --- a/scripts/make_phylogeny.py +++ b/scripts/make_phylogeny.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/make_prefs_file.py b/scripts/make_prefs_file.py index 48be51fa3f..b3137ff002 100755 --- a/scripts/make_prefs_file.py +++ b/scripts/make_prefs_file.py @@ -9,7 +9,7 @@ "Jeremy Widmann", "Antonio Gonzalez Pena"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/scripts/make_qiime_py_file.py b/scripts/make_qiime_py_file.py index 943c8d5b09..a5c2193298 100755 --- a/scripts/make_qiime_py_file.py +++ b/scripts/make_qiime_py_file.py @@ -10,7 +10,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" @@ -88,7 +88,7 @@ def main(): __copyright__ = "COPYRIGHT" __credits__ = ["AUTHOR_NAME"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "AUTHOR_NAME" __email__ = "AUTHOR_EMAIL" """ % strftime('%d %b %Y') diff --git a/scripts/make_rarefaction_plots.py b/scripts/make_rarefaction_plots.py index e114fa3a33..ce2d01c41c 100755 --- a/scripts/make_rarefaction_plots.py +++ b/scripts/make_rarefaction_plots.py @@ -7,7 +7,7 @@ __credits__ = ["Meg Pirrung", "Jesse Stombaugh", "John Chase", "Jai Ram Rideout", "Evan Bolyen"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/scripts/make_tep.py b/scripts/make_tep.py index c71768e613..f94a916d49 100755 --- a/scripts/make_tep.py +++ b/scripts/make_tep.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Meg Pirrung", "Jesse Stombaugh", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Meg Pirrung" __email__ = "meganap@gmail.com" diff --git a/scripts/map_reads_to_reference.py b/scripts/map_reads_to_reference.py index 8f36cd60ee..6a93e0708d 100755 --- a/scripts/map_reads_to_reference.py +++ b/scripts/map_reads_to_reference.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/merge_mapping_files.py b/scripts/merge_mapping_files.py index d7ccb3739a..2832527151 100755 --- a/scripts/merge_mapping_files.py +++ b/scripts/merge_mapping_files.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/merge_otu_maps.py b/scripts/merge_otu_maps.py index 59dd2823fb..c9148f69c8 100755 --- a/scripts/merge_otu_maps.py +++ b/scripts/merge_otu_maps.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Dan Knights"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/merge_otu_tables.py b/scripts/merge_otu_tables.py index d4f40ab44d..8cfbe085dd 100755 --- a/scripts/merge_otu_tables.py +++ b/scripts/merge_otu_tables.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Daniel McDonald"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/multiple_extract_barcodes.py b/scripts/multiple_extract_barcodes.py index 9c6de17142..d4d62c3155 100755 --- a/scripts/multiple_extract_barcodes.py +++ b/scripts/multiple_extract_barcodes.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters", "Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/scripts/multiple_join_paired_ends.py b/scripts/multiple_join_paired_ends.py index 9f99630572..36ad09b5de 100755 --- a/scripts/multiple_join_paired_ends.py +++ b/scripts/multiple_join_paired_ends.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters", "Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/scripts/multiple_rarefactions.py b/scripts/multiple_rarefactions.py index e20c95d61f..6e2d88cbc5 100755 --- a/scripts/multiple_rarefactions.py +++ b/scripts/multiple_rarefactions.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski", "Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/multiple_rarefactions_even_depth.py b/scripts/multiple_rarefactions_even_depth.py index ffc9777693..bc95166fe2 100755 --- a/scripts/multiple_rarefactions_even_depth.py +++ b/scripts/multiple_rarefactions_even_depth.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/multiple_split_libraries_fastq.py b/scripts/multiple_split_libraries_fastq.py index a964bad3ca..0aa9d6613f 100755 --- a/scripts/multiple_split_libraries_fastq.py +++ b/scripts/multiple_split_libraries_fastq.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/scripts/neighbor_joining.py b/scripts/neighbor_joining.py index 627b1acc0a..a5458d00f6 100755 --- a/scripts/neighbor_joining.py +++ b/scripts/neighbor_joining.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/nmds.py b/scripts/nmds.py index c6a68dbd4c..5624e4cc5c 100755 --- a/scripts/nmds.py +++ b/scripts/nmds.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/normalize_table.py b/scripts/normalize_table.py new file mode 100755 index 0000000000..761c8b4081 --- /dev/null +++ b/scripts/normalize_table.py @@ -0,0 +1,125 @@ +#!/usr/bin/env python +# File created on 14 Jul 2014 +from __future__ import division + +from qiime.util import parse_command_line_parameters, make_option +from qiime.normalize_table import normalize_CSS, normalize_DESeq, multiple_file_normalize_CSS, multiple_file_normalize_DESeq, algorithm_list + +import os + +__author__ = "Sophie Weiss" +__copyright__ = "Copyright 2014, The QIIME Project" +__credits__ = ["Sophie Weiss"] +__license__ = "GPL" +__version__ = "1.9.0-rc1" +__maintainer__ = "Sophie Weiss" +__email__ = "sophie.sjw@gmail.com" + +script_info = {} +script_info['brief_description'] = """Matrix normalization alternatives to rarefaction""" +script_info['script_description'] = \ +"""To perform many downstream analyses after OTU picking (besides +metagenomeSeq's fitZIG and DESeq OTU differential abundance testing), the OTU +matrix must be normalized to account for uneven column (sample) sums that are a +result of most modern sequencing techniques. These methods attempt to correct +for compositionality too. Rarefying throws away some data by rarefying to a +constant sum and throwing away extremely low depth samples. + +Even with these new normalization techinques, we would recommend throwing away +low depth samples (e.g. less that 1000 sequences/sample). DESeq outputs +negative values for lower abundant OTUs as a result of its log transformation. +For most ecologically useful metrics (e.g. UniFrac/Bray Curtis) this presents +problems. No good solution exists at the moment for this issue. Note that one +is added to the matrix to avoid log(0). It has been shown that clustering +results can be highly dependent upon the choice of the pseudocount (e.g. should +it be 0.01 instead of 1?), for more information see Costea, P. et al. (2014) +"A fair comparison", Nature Methods. + +DESeq can also have a very slow runtime, especially for larger datasets. +If you do use these alternatives to rarefying, we would only recommend +metagenomeSeq's CSS transformation for those metrics that are abundance-based. +E.g. do not use these new methods for binary Jaccard or unweighted UniFrac. For +more on the methods, please see Paulson, JN, et al. 'Differential abundance +analysis for microbial marker-gene surveys' Nature Methods 2013. For DESeq +please see Anders S, Huber W. 'Differential expression analysis for sequence +count data.' Genome Biology 2010. For any of these methods, clustering by +sequence depth MUST BE CHECKED FOR as a confounding variable, e.g. by coloring +by sequences/sample on a PCoA plot and/or testing for correlations between +taxa abundances and sequencing depth with observation_metadata_correlation.py. +""" + +script_info['script_usage']=[] +script_info['script_usage'].append( + ("CSS Matrix Normalization", + "Normalize a raw (non-normalized/non-rarefied) otu_table.biom using CSS:", + "%prog -i otu_table.biom -a CSS -o CSS_normalized_otu_table.biom")) +script_info['script_usage'].append( + ("DESeq Matrix Normalization", + "Normalize a raw (non-normalized/non-rarefied) otu_table.biom using DESeq:", + "%prog -i otu_table.biom -a DESeq -o DESeq_normalized_otu_table.biom")) +script_info['output_description']= \ +"""BIOM table with normalized counts. Can be used in all downstream analyses +except differential abundance testing and OTU correlations.""" +script_info['required_options']=[] +script_info['optional_options']=[ +make_option('-i', '--input_path', type='existing_path', + help='path to the input BIOM file (e.g., the output ' + 'from OTU picking) or directory containing input BIOM files ' + 'for batch processing [REQUIRED if not passing -l]'), +make_option('-o', '--out_path', type='new_path', + help='output filename for single file operation, or output ' + 'directory for batch processing [REQUIRED if not passing -l]'), +make_option('-s', '--output_CSS_statistics', default=False, + action='store_true', help='output CSS statistics file. This ' + 'will be a directory for batch processing, and a filename for ' + 'single file operation [default: %default]'), +make_option('-z', '--DESeq_negatives_to_zero', default=False, + action='store_true', help='replace negative numbers produced by ' + 'the DESeq normalization technique with zeros [default: ' + '%default]'), +make_option('-a', '--algorithm', default='CSS', type='choice', + choices=algorithm_list(), help='normalization algorithm to apply to input ' + 'BIOM table(s). [default: %default]' + ' Available options are: ' + '%s' % ', '.join(algorithm_list())), +make_option('-l', '--list_algorithms', action='store_true', default=False, + help='show available normalization algorithms and exit ' + '[default: %default]'), + ] +script_info['version'] = __version__ + + + +def main(): + option_parser, opts, args = parse_command_line_parameters(**script_info) + + input_path = opts.input_path + out_path = opts.out_path + output_CSS_statistics = opts.output_CSS_statistics + DESeq_negatives_to_zero = opts.DESeq_negatives_to_zero + algorithm = opts.algorithm + list_algorithms = opts.list_algorithms + + if list_algorithms: + print 'Available normalization algorithms are:\n%s' % ', '.join(algorithm_list()) + elif algorithm == 'CSS': + if os.path.isdir(input_path): + multiple_file_normalize_CSS(input_path, out_path, output_CSS_statistics) + elif os.path.isfile(input_path): + normalize_CSS(input_path, out_path, output_CSS_statistics) + else: + # it shouldn't be possible to get here + option_parser.error("Unknown input type: %s" % input_path) + elif algorithm == 'DESeq': + if os.path.isdir(input_path): + multiple_file_normalize_DESeq(input_path, out_path, DESeq_negatives_to_zero) + elif os.path.isfile(input_path): + normalize_DESeq(input_path, out_path, DESeq_negatives_to_zero) + else: + # it shouldn't be possible to get here + option_parser.error("Unknown input type: %s" % input_path) + else: + # it shouldn't be possible to get here + option_parser.error("Unknown normalization algorithm: %s" % algorithm) + +if __name__ == "__main__": + main() diff --git a/scripts/observation_metadata_correlation.py b/scripts/observation_metadata_correlation.py index cacf9dd428..96b8fb771f 100755 --- a/scripts/observation_metadata_correlation.py +++ b/scripts/observation_metadata_correlation.py @@ -6,7 +6,7 @@ "Jesse Stombaugh", "Doug Wendel", "Dan Knights", "Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Will Van Treuren" __email__ = "wdwvt1@gmail.com" diff --git a/scripts/otu_category_significance.py b/scripts/otu_category_significance.py index e984dc5578..7e5fb1d03f 100755 --- a/scripts/otu_category_significance.py +++ b/scripts/otu_category_significance.py @@ -7,7 +7,7 @@ __credits__ = ["Catherine Lozupone", "Jesse Stombaugh", "Doug Wendel", "Dan Knights", "Greg Caporaso", "Luke Ursell"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Doug Wendel" __email__ = "wendel@colorado.edu" diff --git a/scripts/parallel_align_seqs_pynast.py b/scripts/parallel_align_seqs_pynast.py index 2a197efcb7..9ba8c0d8cf 100755 --- a/scripts/parallel_align_seqs_pynast.py +++ b/scripts/parallel_align_seqs_pynast.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/parallel_alpha_diversity.py b/scripts/parallel_alpha_diversity.py index be270253ef..d324975658 100755 --- a/scripts/parallel_alpha_diversity.py +++ b/scripts/parallel_alpha_diversity.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/parallel_assign_taxonomy_blast.py b/scripts/parallel_assign_taxonomy_blast.py index e123c80439..ca483447b5 100755 --- a/scripts/parallel_assign_taxonomy_blast.py +++ b/scripts/parallel_assign_taxonomy_blast.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/parallel_assign_taxonomy_rdp.py b/scripts/parallel_assign_taxonomy_rdp.py index ed86bbf979..1647e2ce2a 100755 --- a/scripts/parallel_assign_taxonomy_rdp.py +++ b/scripts/parallel_assign_taxonomy_rdp.py @@ -7,7 +7,7 @@ __credits__ = ["Greg Caporaso", "Antonio Gonzalez Pena", "William Walters", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/parallel_assign_taxonomy_uclust.py b/scripts/parallel_assign_taxonomy_uclust.py index b7ca73a55d..2af94f852c 100755 --- a/scripts/parallel_assign_taxonomy_uclust.py +++ b/scripts/parallel_assign_taxonomy_uclust.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/parallel_beta_diversity.py b/scripts/parallel_beta_diversity.py index ccfd23ae3a..3ff1e118bd 100755 --- a/scripts/parallel_beta_diversity.py +++ b/scripts/parallel_beta_diversity.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Jose Antonio Navas Molina", "Emily TerAvest"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/parallel_blast.py b/scripts/parallel_blast.py index c597f33630..3e9eaeba9b 100755 --- a/scripts/parallel_blast.py +++ b/scripts/parallel_blast.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/parallel_identify_chimeric_seqs.py b/scripts/parallel_identify_chimeric_seqs.py index aacbde64f2..c5c3eb22a5 100755 --- a/scripts/parallel_identify_chimeric_seqs.py +++ b/scripts/parallel_identify_chimeric_seqs.py @@ -6,7 +6,7 @@ __credits__ = ["Greg Caporaso", "Jens Reeder", "Jai Ram Rideout", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/parallel_map_reads_to_reference.py b/scripts/parallel_map_reads_to_reference.py index c9878f18a8..ee5e24207e 100755 --- a/scripts/parallel_map_reads_to_reference.py +++ b/scripts/parallel_map_reads_to_reference.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/parallel_merge_otu_tables.py b/scripts/parallel_merge_otu_tables.py index 727c9efcfa..f6772552b2 100755 --- a/scripts/parallel_merge_otu_tables.py +++ b/scripts/parallel_merge_otu_tables.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2013, The QIIME Project" __credits__ = ["Daniel McDonald", "Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Daniel McDonald" __email__ = "mcdonadt@colorado.edu" diff --git a/scripts/parallel_multiple_rarefactions.py b/scripts/parallel_multiple_rarefactions.py index d548afb71f..d2f59b7f8b 100755 --- a/scripts/parallel_multiple_rarefactions.py +++ b/scripts/parallel_multiple_rarefactions.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/parallel_pick_otus_blast.py b/scripts/parallel_pick_otus_blast.py index 2735d17453..92361d1002 100755 --- a/scripts/parallel_pick_otus_blast.py +++ b/scripts/parallel_pick_otus_blast.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Dan Knights", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/parallel_pick_otus_sortmerna.py b/scripts/parallel_pick_otus_sortmerna.py index 85f4dc2003..3f646a262b 100755 --- a/scripts/parallel_pick_otus_sortmerna.py +++ b/scripts/parallel_pick_otus_sortmerna.py @@ -7,7 +7,7 @@ from __future__ import division __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jenya Kopylov" __email__ = "jenya.kopylov@gmail.com" diff --git a/scripts/parallel_pick_otus_trie.py b/scripts/parallel_pick_otus_trie.py index 57ca4b7f3a..710c8608d5 100755 --- a/scripts/parallel_pick_otus_trie.py +++ b/scripts/parallel_pick_otus_trie.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/scripts/parallel_pick_otus_uclust_ref.py b/scripts/parallel_pick_otus_uclust_ref.py index ba24fe361a..66a493c93e 100755 --- a/scripts/parallel_pick_otus_uclust_ref.py +++ b/scripts/parallel_pick_otus_uclust_ref.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/parallel_pick_otus_usearch61_ref.py b/scripts/parallel_pick_otus_usearch61_ref.py index b8ac41f770..48148e8ca0 100755 --- a/scripts/parallel_pick_otus_usearch61_ref.py +++ b/scripts/parallel_pick_otus_usearch61_ref.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/pick_closed_reference_otus.py b/scripts/pick_closed_reference_otus.py index bd658afb8c..4541221866 100755 --- a/scripts/pick_closed_reference_otus.py +++ b/scripts/pick_closed_reference_otus.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/pick_de_novo_otus.py b/scripts/pick_de_novo_otus.py index bae92d0b97..b8b912582e 100755 --- a/scripts/pick_de_novo_otus.py +++ b/scripts/pick_de_novo_otus.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Kyle Bittinger"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/pick_open_reference_otus.py b/scripts/pick_open_reference_otus.py index aaa8a3b4e7..6e40831961 100755 --- a/scripts/pick_open_reference_otus.py +++ b/scripts/pick_open_reference_otus.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/pick_otus.py b/scripts/pick_otus.py index b222814560..5ca0fbaffd 100755 --- a/scripts/pick_otus.py +++ b/scripts/pick_otus.py @@ -8,7 +8,7 @@ "Jens Reeder", "William Walters", "Jose Carlos Clemente Litran", "Jai Ram Rideout", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/pick_rep_set.py b/scripts/pick_rep_set.py index 4862d0c321..2048f4bd00 100755 --- a/scripts/pick_rep_set.py +++ b/scripts/pick_rep_set.py @@ -7,7 +7,7 @@ __credits__ = ["Rob Knight", "Greg Caporaso", "Kyle Bittinger", "Jai Ram Rideout", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Daniel McDonald" __email__ = "wasade@gmail.com" diff --git a/scripts/plot_rank_abundance_graph.py b/scripts/plot_rank_abundance_graph.py index aa256759ec..bf9ae70b47 100755 --- a/scripts/plot_rank_abundance_graph.py +++ b/scripts/plot_rank_abundance_graph.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jens Reeder", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/plot_semivariogram.py b/scripts/plot_semivariogram.py index c2aaf9b693..02b2e94102 100755 --- a/scripts/plot_semivariogram.py +++ b/scripts/plot_semivariogram.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Antonio Gonzalez Pena, Kyle Patnode", "Yoshiki Vazquez-Baeza"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Antonio Gonzalez Pena" __email__ = "antgonza@gmail.com" diff --git a/scripts/plot_taxa_summary.py b/scripts/plot_taxa_summary.py index 3b29f9f7a4..a733a493bb 100755 --- a/scripts/plot_taxa_summary.py +++ b/scripts/plot_taxa_summary.py @@ -7,7 +7,7 @@ __credits__ = ["Jesse Stombaugh", "Julia Goodrich", "Justin Kuczynski", "John Chase", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" """ diff --git a/scripts/poller.py b/scripts/poller.py index ce1e38e3f3..96eae3ada0 100755 --- a/scripts/poller.py +++ b/scripts/poller.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/principal_coordinates.py b/scripts/principal_coordinates.py index 042ffd0753..a6e6797c70 100755 --- a/scripts/principal_coordinates.py +++ b/scripts/principal_coordinates.py @@ -7,7 +7,7 @@ __credits__ = ["Justin Kuczynski", "Rob Knight", "Antonio Gonzalez Pena", "Catherine Lozupone", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Antonio Gonzalez Pena" __email__ = "antgonza@gmail.com" diff --git a/scripts/print_metadata_stats.py b/scripts/print_metadata_stats.py index 2ffd0ef0b7..46f14b4f71 100755 --- a/scripts/print_metadata_stats.py +++ b/scripts/print_metadata_stats.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Daniel McDonald", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Daniel McDonald" __email__ = "mcdonadt@colorado.edu" diff --git a/scripts/print_qiime_config.py b/scripts/print_qiime_config.py index 1ccdf52e73..cca451a2dd 100755 --- a/scripts/print_qiime_config.py +++ b/scripts/print_qiime_config.py @@ -7,7 +7,7 @@ "Justin Kuczynski", "Jai Ram Rideout", "Greg Caporaso", "Emily TerAvest"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/process_iseq.py b/scripts/process_iseq.py index b69ec90180..67d7bc881a 100755 --- a/scripts/process_iseq.py +++ b/scripts/process_iseq.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/process_qseq.py b/scripts/process_qseq.py index 1cef6b7e40..f70881d676 100755 --- a/scripts/process_qseq.py +++ b/scripts/process_qseq.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/process_sff.py b/scripts/process_sff.py index 0d0a61a61a..18f7576157 100755 --- a/scripts/process_sff.py +++ b/scripts/process_sff.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Rob Knight", "Kyle Bittinger", "Jesse Stombaugh"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/scripts/quality_scores_plot.py b/scripts/quality_scores_plot.py index 1db94a71a6..b9e8b6afc8 100755 --- a/scripts/quality_scores_plot.py +++ b/scripts/quality_scores_plot.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/scripts/relatedness.py b/scripts/relatedness.py index 5f059fd64c..c18eea72b6 100755 --- a/scripts/relatedness.py +++ b/scripts/relatedness.py @@ -8,7 +8,7 @@ "Jose Antonio Navas Molina", "Yoshiki Vazquez Baeza", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Van Treuren" __email__ = "wdwvt1@gmail.com" diff --git a/scripts/shared_phylotypes.py b/scripts/shared_phylotypes.py index 582916afbd..d056ac8e52 100755 --- a/scripts/shared_phylotypes.py +++ b/scripts/shared_phylotypes.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jens Reeder"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jose Clemente" __email__ = "jose.clemente@gmail.com" diff --git a/scripts/simsam.py b/scripts/simsam.py index 457244124c..2d7ea375c2 100755 --- a/scripts/simsam.py +++ b/scripts/simsam.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski", "Jai Ram Rideout", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/single_rarefaction.py b/scripts/single_rarefaction.py index 294fd7f14e..76b681eaf7 100755 --- a/scripts/single_rarefaction.py +++ b/scripts/single_rarefaction.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski", "Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/sort_otu_table.py b/scripts/sort_otu_table.py index 930f247cad..b53ee307f8 100755 --- a/scripts/sort_otu_table.py +++ b/scripts/sort_otu_table.py @@ -7,7 +7,7 @@ __credits__ = ["Greg Caporaso", "Daniel McDonald", "Emily TerAvest", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/split_libraries.py b/scripts/split_libraries.py index 6ac2e298bc..2381929b69 100755 --- a/scripts/split_libraries.py +++ b/scripts/split_libraries.py @@ -9,7 +9,7 @@ "Jens Reeder", "Jose Antonio Navas Molina", "Jai Ram Rideout"] # remember to add yourself __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Walters" __email__ = "william.a.walters@colorado.edu" diff --git a/scripts/split_libraries_fastq.py b/scripts/split_libraries_fastq.py index b228343b9f..f59a6dc9bf 100755 --- a/scripts/split_libraries_fastq.py +++ b/scripts/split_libraries_fastq.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Emily TerAvest"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/split_libraries_lea_seq.py b/scripts/split_libraries_lea_seq.py index 166dcd2a7f..d410e61334 100755 --- a/scripts/split_libraries_lea_seq.py +++ b/scripts/split_libraries_lea_seq.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2014, The QIIME Project" __credits__ = ["Charudatta Navare", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Charudatta Navare" __email__ = "charudatta.navare@gmail.com" diff --git a/scripts/split_otu_table.py b/scripts/split_otu_table.py index 7ad6c9129b..d7d2df2c46 100755 --- a/scripts/split_otu_table.py +++ b/scripts/split_otu_table.py @@ -7,7 +7,7 @@ __credits__ = ["Greg Caporaso", "Antonio Gonzalez Pena", "Yoshiki Vazquez Baeza", "Will Van Treuren"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/split_otu_table_by_taxonomy.py b/scripts/split_otu_table_by_taxonomy.py index 478c747aa0..320b4db3a8 100755 --- a/scripts/split_otu_table_by_taxonomy.py +++ b/scripts/split_otu_table_by_taxonomy.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2010, The QIIME project" __credits__ = ["Greg Caporaso", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/split_sequence_file_on_sample_ids.py b/scripts/split_sequence_file_on_sample_ids.py index 50e281b3db..e93cff15a9 100755 --- a/scripts/split_sequence_file_on_sample_ids.py +++ b/scripts/split_sequence_file_on_sample_ids.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/start_parallel_jobs.py b/scripts/start_parallel_jobs.py index c830a5c602..883c01fc75 100755 --- a/scripts/start_parallel_jobs.py +++ b/scripts/start_parallel_jobs.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/start_parallel_jobs_sc.py b/scripts/start_parallel_jobs_sc.py index 6bec635d34..595cee47d4 100755 --- a/scripts/start_parallel_jobs_sc.py +++ b/scripts/start_parallel_jobs_sc.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/start_parallel_jobs_torque.py b/scripts/start_parallel_jobs_torque.py index 9937c2eaf5..4711d20a37 100755 --- a/scripts/start_parallel_jobs_torque.py +++ b/scripts/start_parallel_jobs_torque.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jens Reeder", "Rob Knight", "Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/subsample_fasta.py b/scripts/subsample_fasta.py index c933ac0132..b7dac14c31 100755 --- a/scripts/subsample_fasta.py +++ b/scripts/subsample_fasta.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Walters" __email__ = "william.a.walters@gmail.com" diff --git a/scripts/summarize_taxa.py b/scripts/summarize_taxa.py index 86786ce5e5..c00645db0f 100755 --- a/scripts/summarize_taxa.py +++ b/scripts/summarize_taxa.py @@ -9,7 +9,7 @@ "Jesse Stombaugh", "Jose Carlos Clemente Litran", "Greg Caporaso", "Jai Ram Rideout", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Daniel McDonald" __email__ = "wasade@gmail.com" diff --git a/scripts/summarize_taxa_through_plots.py b/scripts/summarize_taxa_through_plots.py index 918c8836b7..bea9c8aa32 100755 --- a/scripts/summarize_taxa_through_plots.py +++ b/scripts/summarize_taxa_through_plots.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Jesse Stombaugh"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/scripts/supervised_learning.py b/scripts/supervised_learning.py index 1f444f06ab..c95e1f16b8 100755 --- a/scripts/supervised_learning.py +++ b/scripts/supervised_learning.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Dan Knights", "Luke Ursell"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Dan Knights" __email__ = "daniel.knights@colorado.edu" diff --git a/scripts/transform_coordinate_matrices.py b/scripts/transform_coordinate_matrices.py index 8350b49c96..8c26adc572 100755 --- a/scripts/transform_coordinate_matrices.py +++ b/scripts/transform_coordinate_matrices.py @@ -7,7 +7,7 @@ __credits__ = ["Greg Caporaso", "Justin Kuczynski", "Jose Carlos Clemente Litran", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/tree_compare.py b/scripts/tree_compare.py index 4cf73476d5..2ff0d856ba 100755 --- a/scripts/tree_compare.py +++ b/scripts/tree_compare.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/trflp_file_to_otu_table.py b/scripts/trflp_file_to_otu_table.py index d61b93f79b..757f23012a 100755 --- a/scripts/trflp_file_to_otu_table.py +++ b/scripts/trflp_file_to_otu_table.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Antonio Gonzalez Pena", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Antonio Gonzalez Pena" __email__ = "antgonza@gmail.com" diff --git a/scripts/trim_sff_primers.py b/scripts/trim_sff_primers.py index f80da0de37..6834a226a1 100755 --- a/scripts/trim_sff_primers.py +++ b/scripts/trim_sff_primers.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Rob Knight", "Kyle Bittinger"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/scripts/truncate_fasta_qual_files.py b/scripts/truncate_fasta_qual_files.py index b36b5c3430..4366fcbbbb 100755 --- a/scripts/truncate_fasta_qual_files.py +++ b/scripts/truncate_fasta_qual_files.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/scripts/truncate_reverse_primer.py b/scripts/truncate_reverse_primer.py index ea70eb9286..b24c2dc064 100755 --- a/scripts/truncate_reverse_primer.py +++ b/scripts/truncate_reverse_primer.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/scripts/unweight_fasta.py b/scripts/unweight_fasta.py index a84e620300..583afc21fd 100755 --- a/scripts/unweight_fasta.py +++ b/scripts/unweight_fasta.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/upgma_cluster.py b/scripts/upgma_cluster.py index 7759edeefc..33b126c007 100755 --- a/scripts/upgma_cluster.py +++ b/scripts/upgma_cluster.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/validate_demultiplexed_fasta.py b/scripts/validate_demultiplexed_fasta.py index 20b0d6c07f..950d762831 100755 --- a/scripts/validate_demultiplexed_fasta.py +++ b/scripts/validate_demultiplexed_fasta.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Anton Walters"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Anton Walters" __email__ = "william.a.walters@gmail.com" diff --git a/scripts/validate_mapping_file.py b/scripts/validate_mapping_file.py index 70be13dc21..5511d49fb8 100755 --- a/scripts/validate_mapping_file.py +++ b/scripts/validate_mapping_file.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/setup.py b/setup.py index e04a4c1754..3622c9b7c5 100644 --- a/setup.py +++ b/setup.py @@ -17,7 +17,7 @@ __credits__ = ["Greg Caporaso", "Kyle Bittinger", "Jai Ram Rideout", "Yoshiki Vazquez Baeza", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "qiime.help@gmail.com" diff --git a/tests/__init__.py b/tests/__init__.py index 7f1577235d..b9584fc8c4 100644 --- a/tests/__init__.py +++ b/tests/__init__.py @@ -16,7 +16,7 @@ "Daniel McDonald", "Catherine Lozupone"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" __status__ = "Development" diff --git a/tests/all_tests.py b/tests/all_tests.py index e49a3ee44b..efafa1045e 100755 --- a/tests/all_tests.py +++ b/tests/all_tests.py @@ -17,7 +17,7 @@ __credits__ = ["Rob Knight", "Greg Caporaso", "Jai Ram Rideout", "Yoshiki Vazquez Baeza"] # remember to add yourself if you make changes __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_add_alpha_to_mapping_file.py b/tests/test_add_alpha_to_mapping_file.py index 02ac08075d..ab3bd4cff0 100755 --- a/tests/test_add_alpha_to_mapping_file.py +++ b/tests/test_add_alpha_to_mapping_file.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Yoshiki Vazquez-Baeza"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Yoshiki Vazquez-Baeza" __email__ = "yoshiki89@gmail.com" diff --git a/tests/test_add_qiime_labels.py b/tests/test_add_qiime_labels.py index d6ea141a82..c44edf3fa5 100755 --- a/tests/test_add_qiime_labels.py +++ b/tests/test_add_qiime_labels.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters"] # remember to add yourself __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Walters" __email__ = "william.a.walters@colorado.edu" diff --git a/tests/test_adjust_seq_orientation.py b/tests/test_adjust_seq_orientation.py index 80493681da..3b60cc1293 100755 --- a/tests/test_adjust_seq_orientation.py +++ b/tests/test_adjust_seq_orientation.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_align_seqs.py b/tests/test_align_seqs.py index 72d685b4ca..435d7ae01e 100644 --- a/tests/test_align_seqs.py +++ b/tests/test_align_seqs.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jeremy Widmann"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_alpha_diversity.py b/tests/test_alpha_diversity.py index 4e8666f1f0..77b65bb3e9 100644 --- a/tests/test_alpha_diversity.py +++ b/tests/test_alpha_diversity.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski", "Rob Knight", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_assign_taxonomy.py b/tests/test_assign_taxonomy.py index 2f51d08a5e..d947a5098a 100644 --- a/tests/test_assign_taxonomy.py +++ b/tests/test_assign_taxonomy.py @@ -8,7 +8,7 @@ __credits__ = ["Greg Caporaso", "Kyle Bittinger", "David Soergel", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_barcode.py b/tests/test_barcode.py index 75def67658..43c010ec22 100644 --- a/tests/test_barcode.py +++ b/tests/test_barcode.py @@ -5,7 +5,7 @@ # remember to add yourself if you make changes __credits__ = ["Justin Kuczynski", "Rob Knight"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_beta_diversity.py b/tests/test_beta_diversity.py index b9398a358a..b9e6240835 100644 --- a/tests/test_beta_diversity.py +++ b/tests/test_beta_diversity.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski", "Rob Knight", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_beta_metrics.py b/tests/test_beta_metrics.py index 4e14d09d94..e7b3222ede 100644 --- a/tests/test_beta_metrics.py +++ b/tests/test_beta_metrics.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Rob Knight", "Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "justin kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_biplots.py b/tests/test_biplots.py index 34eb7db903..5d97409e60 100755 --- a/tests/test_biplots.py +++ b/tests/test_biplots.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_categorized_dist_scatterplot.py b/tests/test_categorized_dist_scatterplot.py index 9b80c9cbe0..5e063d75ac 100755 --- a/tests/test_categorized_dist_scatterplot.py +++ b/tests/test_categorized_dist_scatterplot.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_clean_raxml_parsimony_tree.py b/tests/test_clean_raxml_parsimony_tree.py index 94e90836d6..bc9500e89c 100755 --- a/tests/test_clean_raxml_parsimony_tree.py +++ b/tests/test_clean_raxml_parsimony_tree.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Jesse Stombaugh"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/tests/test_cluster_quality.py b/tests/test_cluster_quality.py index 5f00587779..78b10c6894 100644 --- a/tests/test_cluster_quality.py +++ b/tests/test_cluster_quality.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_collate_alpha.py b/tests/test_collate_alpha.py index bfdd725106..039b1b6d59 100644 --- a/tests/test_collate_alpha.py +++ b/tests/test_collate_alpha.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["justin kuczynski"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_colors.py b/tests/test_colors.py index 5e59103627..9f6b125f34 100644 --- a/tests/test_colors.py +++ b/tests/test_colors.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" # consider project name __credits__ = ["Jesse Stombaugh"] # remember to add yourself __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/tests/test_compare_alpha_diversity.py b/tests/test_compare_alpha_diversity.py index 1af525e6a2..920bf6021e 100755 --- a/tests/test_compare_alpha_diversity.py +++ b/tests/test_compare_alpha_diversity.py @@ -7,7 +7,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["William Van Treuren", "Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Van Treuren" __email__ = "vantreur@colorado.edu" diff --git a/tests/test_compare_categories.py b/tests/test_compare_categories.py index 54d61b48ec..d3833433cb 100644 --- a/tests/test_compare_categories.py +++ b/tests/test_compare_categories.py @@ -6,7 +6,7 @@ __credits__ = ["Jai Ram Rideout", "Michael Dwan", "Logan Knecht", "Damien Coy", "Levi McCracken"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/tests/test_compare_distance_matrices.py b/tests/test_compare_distance_matrices.py index 2b47bf325e..62dded402f 100644 --- a/tests/test_compare_distance_matrices.py +++ b/tests/test_compare_distance_matrices.py @@ -6,7 +6,7 @@ __credits__ = ["Jai Ram Rideout", "Michael Dwan", "Logan Knecht", "Damien Coy", "Levi McCracken"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/tests/test_compare_taxa_summaries.py b/tests/test_compare_taxa_summaries.py index 7c83194815..498a0cf3e0 100644 --- a/tests/test_compare_taxa_summaries.py +++ b/tests/test_compare_taxa_summaries.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2012, The QIIME project" __credits__ = ["Jai Ram Rideout", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/tests/test_compare_trajectories.py b/tests/test_compare_trajectories.py index 9de3c6caa4..ec2a6ab85f 100644 --- a/tests/test_compare_trajectories.py +++ b/tests/test_compare_trajectories.py @@ -6,7 +6,7 @@ __credits__ = ["Jose Antonio Navas Molina", "Antonio Gonzalez Pena", "Yoshiki Vazquez Baeza", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jose Antonio Navas Molina" __email__ = "josenavasmolina@gmail.com" diff --git a/tests/test_compute_taxonomy_ratios.py b/tests/test_compute_taxonomy_ratios.py index 6bfa287bfc..6d37daf0fb 100644 --- a/tests/test_compute_taxonomy_ratios.py +++ b/tests/test_compute_taxonomy_ratios.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2014, The QIIME Project" __credits__ = ["Daniel McDonald"] __license__ = "BSD" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Daniel McDonald" __email__ = "mcdonadt@colorado.edu" diff --git a/tests/test_convert_fastaqual_fastq.py b/tests/test_convert_fastaqual_fastq.py index 58a4792658..6023d3189f 100755 --- a/tests/test_convert_fastaqual_fastq.py +++ b/tests/test_convert_fastaqual_fastq.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Adam Robbins-Pianka", "Abhisaar Yadav", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Adam Robbins-Pianka" __email__ = "adam.robbinspianka@colorado.edu" diff --git a/tests/test_core_microbiome.py b/tests/test_core_microbiome.py index d66ccefbee..b733ca09a8 100755 --- a/tests/test_core_microbiome.py +++ b/tests/test_core_microbiome.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_demultiplex_fasta.py b/tests/test_demultiplex_fasta.py index 79c426fe0c..83e93121cc 100755 --- a/tests/test_demultiplex_fasta.py +++ b/tests/test_demultiplex_fasta.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Rob Knight", "William Walters"] # remember to add yourself __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Walters" __email__ = "william.a.walters@colorado.edu" diff --git a/tests/test_denoise_wrapper.py b/tests/test_denoise_wrapper.py index b543ce5c40..e996263d69 100644 --- a/tests/test_denoise_wrapper.py +++ b/tests/test_denoise_wrapper.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_denoiser/test_cluster_util.py b/tests/test_denoiser/test_cluster_util.py index 4a3361cafd..ba4680aa5a 100644 --- a/tests/test_denoiser/test_cluster_util.py +++ b/tests/test_denoiser/test_cluster_util.py @@ -6,7 +6,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/tests/test_denoiser/test_denoise_postprocess.py b/tests/test_denoiser/test_denoise_postprocess.py index fb58206135..7677163466 100644 --- a/tests/test_denoiser/test_denoise_postprocess.py +++ b/tests/test_denoiser/test_denoise_postprocess.py @@ -8,7 +8,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/tests/test_denoiser/test_denoiser.py b/tests/test_denoiser/test_denoiser.py index 068636999e..1ee6c73bd7 100644 --- a/tests/test_denoiser/test_denoiser.py +++ b/tests/test_denoiser/test_denoiser.py @@ -8,7 +8,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/tests/test_denoiser/test_flowgram_clustering.py b/tests/test_denoiser/test_flowgram_clustering.py index 38e96d0ce0..87250c350b 100644 --- a/tests/test_denoiser/test_flowgram_clustering.py +++ b/tests/test_denoiser/test_flowgram_clustering.py @@ -6,7 +6,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight", "Nigel Cook"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/tests/test_denoiser/test_flowgram_filter.py b/tests/test_denoiser/test_flowgram_filter.py index 76499d9f6f..f711896c9c 100644 --- a/tests/test_denoiser/test_flowgram_filter.py +++ b/tests/test_denoiser/test_flowgram_filter.py @@ -6,7 +6,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/tests/test_denoiser/test_make_cluster_jobs.py b/tests/test_denoiser/test_make_cluster_jobs.py index 794a5a2707..bf0871991c 100644 --- a/tests/test_denoiser/test_make_cluster_jobs.py +++ b/tests/test_denoiser/test_make_cluster_jobs.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/tests/test_denoiser/test_preprocess.py b/tests/test_denoiser/test_preprocess.py index df9e5acb05..4e79a34244 100644 --- a/tests/test_denoiser/test_preprocess.py +++ b/tests/test_denoiser/test_preprocess.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/tests/test_denoiser/test_settings.py b/tests/test_denoiser/test_settings.py index 2942b59d09..6fbf482985 100644 --- a/tests/test_denoiser/test_settings.py +++ b/tests/test_denoiser/test_settings.py @@ -8,7 +8,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/tests/test_denoiser/test_utils.py b/tests/test_denoiser/test_utils.py index 9e718ed86a..3eb9b841e4 100644 --- a/tests/test_denoiser/test_utils.py +++ b/tests/test_denoiser/test_utils.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/tests/test_detrend.py b/tests/test_detrend.py index 69a40ecc04..dcd9c05714 100644 --- a/tests/test_detrend.py +++ b/tests/test_detrend.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Dan Knights"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Dan Knights" __email__ = "daniel.knights@colorado.edu" diff --git a/tests/test_differential_abundance.py b/tests/test_differential_abundance.py new file mode 100644 index 0000000000..5335851270 --- /dev/null +++ b/tests/test_differential_abundance.py @@ -0,0 +1,200 @@ +#!/usr/bin/env python + +from os import close +from shutil import rmtree +from tempfile import mkstemp + +from unittest import TestCase, main +from biom import load_table + +from skbio.util import remove_files +from qiime.util import load_qiime_config +from qiime.differential_abundance import DA_fitZIG, DA_DESeq2 + + +__author__ = "Sophie Weiss" +__copyright__ = "Copyright 2014, The QIIME Project" +__credits__ = ["Sophie Weiss"] +__license__ = "GPL" +__version__ = "1.9.0-rc1" +__maintainer__ = "Sophie Weiss" +__email__ = "sophie.sjw@gmail.com" + +"""Contains tests for the output of DESeq2 negative binomial and metagenomeSeq fitZIG OTU differential abundance testing. modeled after test_supervised_learning.py""" + + +def is_float(input_string): + """True if string can be cast as a float""" + try: + float(input_string) + return True + except ValueError: + return False + +class RDifferentialAbundanceTests(TestCase): + + """Tests of the RDifferentialAbundanceTest class""" + + def setUp(self): + self.qiime_config = load_qiime_config() + self.tmp_dir = self.qiime_config['temp_dir'] or '/tmp/' + + # Temporary input file + fd, self.tmp_otu_fp = mkstemp(dir=self.tmp_dir, + prefix='R_test_otu_table_', + suffix='.biom') + close(fd) + seq_file = open(self.tmp_otu_fp, 'w') + seq_file.write(test_otu_table) + seq_file.close() + + fd, self.tmp_map_fp = mkstemp(dir=self.tmp_dir, + prefix='R_test_map_', + suffix='.txt') + close(fd) + seq_file = open(self.tmp_map_fp, 'w') + seq_file.write(test_map) + seq_file.close() + + fd, self.tmp_otu_fp_fitZIG_out = mkstemp(dir=self.tmp_dir, + prefix='R_test_otu_table_fitZIG_out_', + suffix='.txt') + fd, self.tmp_otu_fp_DESeq2_out = mkstemp(dir=self.tmp_dir, + prefix='R_test_otu_table_DESeq2_out_', + suffix='.txt') + + self.files_to_remove = \ + [self.tmp_otu_fp, self.tmp_map_fp, self.tmp_otu_fp_fitZIG_out, self.tmp_otu_fp_DESeq2_out] + + DA_fitZIG(self.tmp_otu_fp, self.tmp_otu_fp_fitZIG_out, self.tmp_map_fp, 'Individual', 'S1', 'S2') + DA_DESeq2(self.tmp_otu_fp, self.tmp_otu_fp_DESeq2_out, self.tmp_map_fp, 'Individual', 'S1', 'S2', DESeq2_diagnostic_plots=False) + + def test_metagenomeSeq_fitZIG_format(self): + zig = open(self.tmp_otu_fp_fitZIG_out).readlines() + #test header format + exp = 'Taxa\t+samples in group 0\t+samples in group 1\tcounts in group 0\tcounts in group 1\toddsRatio\tlower\tupper\tfisherP\tfisherAdjP\t(Intercept)\tMGS_categoryS2\tMGS_categoryS3\tscalingFactor\tpvalues\tadjPvalues' + self.assertEqual(zig[0].strip(), exp) + + #test that fitZIG returns 25 features, it only returns the most important + num_features_returned = len(zig) - 1 + self.assertEqual(num_features_returned, 25) + + # ensure that each line has two elements, and that the first one + # is the name of one of the OTUs, the second is a float + for line in zig[1:]: + words = line.strip().split('\t') + line_length = len(words) + self.assertEqual(line_length, 16) + self.assertEqual(words[0] in test_OTU_IDs, True) + self.assertEqual(is_float(words[1]), True) + + #test first five significant OTUs + exp = ['1487\t3\t13\t3\t54\t0\t0\t0.0814754160126085\t1.03417385089143e-07\t2.58543462722858e-06\t0.732914457135622\t2.35091578797182\t-0.358285072078857\t-28.0403903601361\t2.59620832179624e-05\t0.000649052080449059\n', + '193\t2\t10\t4\t25\t0.0308298124876527\t0.00223706309126031\t0.229093863501484\t3.241507131278e-05\t0.000135062797136583\t0.980060835463344\t2.05824256013173\t-0.393172554812399\t-43.9276179169663\t6.26549562011497e-05\t0.000783186952514372\n', + '979\t0\t10\t0\t20\t0\t0\t0.0956087104342576\t6.04991702771485e-07\t5.04159752309571e-06\t0.0855575301280384\t1.4678274119766\t0.00901541795158288\t-7.07862887279825\t0.000648824231851767\t0.00540686859876472\n', + '1314\t4\t0\t7\t0\tInf\t0.34924924266116\tInf\t0.277924541082436\t0.347405676353045\t0.412980602558517\t-1.25800421238268\t-0.711956542078996\t22.3778549863952\t0.00315666606837298\t0.0197291629273311\n', + '1351\t0\t6\t0\t12\t0\t0\t0.320469784786932\t0.000621585760904647\t0.00194245550282702\t0.106944586260241\t1.21145998904839\t0.0112690273007214\t-8.84809361558598\t0.00579444501011918\t0.0289722250505959\n'] + for a, e in zip(zig[1:6],exp): + af = map(float,a.split('\t')) + ef = map(float,e.split('\t')) + self.assertEqual(len(af), len(ef)) + for af_e, ef_e in zip(af, ef): + self.assertAlmostEqual(af_e, ef_e) + + def test_DESeq2_nbinom_format(self): + nbinom = open(self.tmp_otu_fp_DESeq2_out).readlines() + #test header format + exp = 'OTU\tbaseMean\tlog2FoldChange\tlfcSE\tstat\tpvalue\tpadj' + self.assertEqual(nbinom[0].strip(), exp) + + #test that all features in input biom table returned + num_features_returned = len(nbinom) - 1 + self.assertEqual(num_features_returned, 50) + + # ensure that each line has seven elements, and that the first one + # is the name of one of the OTUs, the second is a float + for line in nbinom[1:]: + words = line.strip().split('\t') + line_length = len(words) + self.assertEqual(line_length, 7) + self.assertEqual(words[0] in test_OTU_IDs, True) + self.assertEqual(is_float(words[1]), True) + + #test first five significant OTUs + exp=['1848\t119.050214384222\t2.9560510780622\t0.27609765938806\t10.706541607828\t9.48387951847218e-27\t2.84516385554165e-25\n', + '2096\t4.57782752174272\t-2.51043602053873\t0.534006762361075\t-4.7011315164606\t2.58723804969022e-06\t3.88085707453532e-05\n', + '2366\t3.63266497414694\t-2.21660628894061\t0.514240606913112\t-4.31044584799803\t1.62925724104894e-05\t0.000162925724104894\n', + '1088\t2.80571100244187\t-1.9610730170819\t0.485853003903793\t-4.03635050380428\t5.42890917069973e-05\t0.00040716818780248\n', + '3006\t2.62956013500845\t-1.73771036728344\t0.489095213973481\t-3.55290814065839\t0.000380997482497004\t0.00228598489498202\n'] + for a, e in zip(nbinom[1:6],exp): + af = map(float,a.split('\t')) + ef = map(float,e.split('\t')) + self.assertEqual(len(af), len(ef)) + for af_e, ef_e in zip(af, ef): + self.assertAlmostEqual(af_e, ef_e) + + def tearDown(self): + """cleanup temporary files and dirs + """ + remove_files(set(self.files_to_remove)) + + +test_OTU_IDs = ['88', + '131', + '144', + '158', + '193', + '225', + '260', + '588', + '634', + '721', + '821', + '843', + '883', + '891', + '976', + '979', + '983', + '1035', + '1088', + '1156', + '1287', + '1314', + '1351', + '1373', + '1487', + '1582', + '1591', + '1784', + '1848', + '1886', + '2007', + '2059', + '2096', + '2187', + '2218', + '2270', + '2328', + '2360', + '2366', + '2407', + '2519', + '2526', + '2810', + '2915', + '2932', + '2956', + '3006', + '3060', + '3108', + '3127'] + +test_otu_table = """{"rows": [{"id": "88", "metadata": {"taxonomy": ["Aa", "other"]}}, {"id": "131", "metadata": {"taxonomy": ["Ab", "other"]}}, {"id": "144", "metadata": {"taxonomy": ["Ac", "other"]}}, {"id": "158", "metadata": {"taxonomy": ["Ad", "other"]}}, {"id": "193", "metadata": {"taxonomy": ["Ae", "other"]}}, {"id": "225", "metadata": {"taxonomy": ["Af", "other"]}}, {"id": "260", "metadata": {"taxonomy": ["Ag", "other"]}}, {"id": "588", "metadata": {"taxonomy": ["Ah", "other"]}}, {"id": "634", "metadata": {"taxonomy": ["Ai", "other"]}}, {"id": "721", "metadata": {"taxonomy": ["Aj", "other"]}}, {"id": "821", "metadata": {"taxonomy": ["Ak", "other"]}}, {"id": "843", "metadata": {"taxonomy": ["Al", "other"]}}, {"id": "883", "metadata": {"taxonomy": ["Am", "other"]}}, {"id": "891", "metadata": {"taxonomy": ["An", "other"]}}, {"id": "976", "metadata": {"taxonomy": ["Ao", "other"]}}, {"id": "979", "metadata": {"taxonomy": ["Ap", "other"]}}, {"id": "983", "metadata": {"taxonomy": ["Aq", "other"]}}, {"id": "1035", "metadata": {"taxonomy": ["Ar", "other"]}}, {"id": "1088", "metadata": {"taxonomy": ["As", "other"]}}, {"id": "1156", "metadata": {"taxonomy": ["At", "other"]}}, {"id": "1287", "metadata": {"taxonomy": ["Au", "other"]}}, {"id": "1314", "metadata": {"taxonomy": ["Av", "other"]}}, {"id": "1351", "metadata": {"taxonomy": ["Aw", "other"]}}, {"id": "1373", "metadata": {"taxonomy": ["Ax", "other"]}}, {"id": "1487", "metadata": {"taxonomy": ["Ay", "other"]}}, {"id": "1582", "metadata": {"taxonomy": ["Az", "other"]}}, {"id": "1591", "metadata": {"taxonomy": ["Ba", "other"]}}, {"id": "1784", "metadata": {"taxonomy": ["Bb", "other"]}}, {"id": "1848", "metadata": {"taxonomy": ["Bc", "other"]}}, {"id": "1886", "metadata": {"taxonomy": ["Bd", "other"]}}, {"id": "2007", "metadata": {"taxonomy": ["Be", "other"]}}, {"id": "2059", "metadata": {"taxonomy": ["Bf", "other"]}}, {"id": "2096", "metadata": {"taxonomy": ["Bg", "other"]}}, {"id": "2187", "metadata": {"taxonomy": ["Bh", "other"]}}, {"id": "2218", "metadata": {"taxonomy": ["Bi", "other"]}}, {"id": "2270", "metadata": {"taxonomy": ["Bj", "other"]}}, {"id": "2328", "metadata": {"taxonomy": ["Bk", "other"]}}, {"id": "2360", "metadata": {"taxonomy": ["Bl", "other"]}}, {"id": "2366", "metadata": {"taxonomy": ["Bm", "other"]}}, {"id": "2407", "metadata": {"taxonomy": ["Bn", "other"]}}, {"id": "2519", "metadata": {"taxonomy": ["Bo", "other"]}}, {"id": "2526", "metadata": {"taxonomy": ["Bp", "other"]}}, {"id": "2810", "metadata": {"taxonomy": ["Bq", "other"]}}, {"id": "2915", "metadata": {"taxonomy": ["Br", "other"]}}, {"id": "2932", "metadata": {"taxonomy": ["Bs", "other"]}}, {"id": "2956", "metadata": {"taxonomy": ["Bt", "other"]}}, {"id": "3006", "metadata": {"taxonomy": ["Bu", "other"]}}, {"id": "3060", "metadata": {"taxonomy": ["Bv", "other"]}}, {"id": "3108", "metadata": {"taxonomy": ["Bw", "other"]}}, {"id": "3127", "metadata": {"taxonomy": ["Bx", "other"]}}], "format": "Biological Observation Matrix v0.9", "data": [[0, 13, 1.0], [0, 14, 4.0], [0, 15, 2.0], [0, 17, 3.0], [0, 18, 4.0], [0, 19, 3.0], [0, 22, 1.0], [0, 23, 5.0], [0, 24, 3.0], [0, 25, 3.0], [0, 26, 1.0], [0, 27, 1.0], [0, 28, 1.0], [0, 29, 1.0], [0, 30, 2.0], [0, 31, 1.0], [0, 35, 1.0], [0, 37, 1.0], [1, 9, 1.0], [1, 12, 1.0], [1, 13, 1.0], [1, 14, 1.0], 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29, 1.0], [49, 30, 2.0], [49, 35, 1.0]], "columns": [{"id": "S1RingL", "metadata": null}, {"id": "S1keyM", "metadata": null}, {"id": "S1keySpace", "metadata": null}, {"id": "S1IndexL", "metadata": null}, {"id": "S1keyK", "metadata": null}, {"id": "S1ThumbR", "metadata": null}, {"id": "S1keyV", "metadata": null}, {"id": "S1IndexR", "metadata": null}, {"id": "S1keyA", "metadata": null}, {"id": "S1RingR", "metadata": null}, {"id": "S1MiddleR", "metadata": null}, {"id": "S1keyD", "metadata": null}, {"id": "S2keySpace", "metadata": null}, {"id": "S2keyJ", "metadata": null}, {"id": "S2keyLeftShift", "metadata": null}, {"id": "S2keyN", "metadata": null}, {"id": "S2keyZ", "metadata": null}, {"id": "S2IndexL", "metadata": null}, {"id": "S2keyA", "metadata": null}, {"id": "S2PinkyL", "metadata": null}, {"id": "S2keyK", "metadata": null}, {"id": "S2keyRightShift", "metadata": null}, {"id": "S2keyM", "metadata": null}, {"id": "S2keyI", "metadata": null}, {"id": "S2PinkyR", "metadata": null}, {"id": "S3keySpace", "metadata": null}, {"id": "S3keyEnter", "metadata": null}, {"id": "S3keyS", "metadata": null}, {"id": "S3IndexR", "metadata": null}, {"id": "S3ThumbR", "metadata": null}, {"id": "S3MiddleR", "metadata": null}, {"id": "S3keyY", "metadata": null}, {"id": "S3ThumbL", "metadata": null}, {"id": "S3keyF", "metadata": null}, {"id": "S3IndexL", "metadata": null}, {"id": "S3keyW", "metadata": null}, {"id": "S3keyQ", "metadata": null}, {"id": "S3keyL", "metadata": null}], "generated_by": "QIIME 1.4.0-dev, svn revision 2595", "matrix_type": "sparse", "shape": [50, 38], "format_url": "http://www.qiime.org/svn_documentation/documentation/biom_format.html", "date": "2011-12-22T01:46:08.091846", "type": "OTU table", "id": null, "matrix_element_type": "float"}""" + + +test_map=\ +'#SampleID\tBarcodeSequence\tLinkerPrimerSequence\tIndividual\tDescription\rS1RingL\t\t\tS1\t"QIIME test code mapping file, similar to that in supervised_learning.py"\rS1keyM\t\t\tS1\t"QIIME test code mapping file, similar to that in supervised_learning.py"\rS1keySpace\t\t\tS1\t"QIIME test code mapping file, similar to that in supervised_learning.py"\rS1IndexL\t\t\tS1\t"QIIME test code mapping file, similar to that in supervised_learning.py"\rS1keyK\t\t\tS1\t"QIIME test code mapping file, similar to that in supervised_learning.py"\rS1ThumbR\t\t\tS1\t"QIIME test code mapping file, similar to that in supervised_learning.py"\rS1keyV\t\t\tS1\t"QIIME test code mapping file, similar to that in supervised_learning.py"\rS1IndexR\t\t\tS1\t"QIIME test code mapping file, similar to that in supervised_learning.py"\rS1keyA\t\t\tS1\t"QIIME test code mapping file, similar to that in supervised_learning.py"\rS1RingR\t\t\tS1\t"QIIME test code mapping file, similar to that in supervised_learning.py"\rS1MiddleR\t\t\tS1\t"QIIME test code mapping file, similar to that in supervised_learning.py"\rS1keyD\t\t\tS1\t"QIIME test code mapping file, similar to that in supervised_learning.py"\rS2keySpace\t\t\tS2\t"QIIME test code mapping file, similar to that in supervised_learning.py"\rS2keyJ\t\t\tS2\t"QIIME test code mapping file, similar to that in supervised_learning.py"\rS2keyLeftShift\t\t\tS2\t"QIIME test code mapping file, similar to that in supervised_learning.py"\rS2keyN\t\t\tS2\t"QIIME test code mapping file, similar to that in supervised_learning.py"\rS2keyZ\t\t\tS2\t"QIIME test code mapping file, similar to that in supervised_learning.py"\rS2IndexL\t\t\tS2\t"QIIME test code mapping file, similar to that in supervised_learning.py"\rS2keyA\t\t\tS2\t"QIIME test code mapping file, similar to that in supervised_learning.py"\rS2PinkyL\t\t\tS2\t"QIIME test code mapping file, similar to that in supervised_learning.py"\rS2keyK\t\t\tS2\t"QIIME test code mapping file, similar to that in supervised_learning.py"\rS2keyRightShift\t\t\tS2\t"QIIME test code mapping file, similar to that in supervised_learning.py"\rS2keyM\t\t\tS2\t"QIIME test code mapping file, similar to that in supervised_learning.py"\rS2keyI\t\t\tS2\t"QIIME test code mapping file, similar to that in supervised_learning.py"\rS2PinkyR\t\t\tS2\t"QIIME test code mapping file, similar to that in supervised_learning.py"\rS3keySpace\t\t\tS3\t"QIIME test code mapping file, similar to that in supervised_learning.py"\rS3keyEnter\t\t\tS3\t"QIIME test code mapping file, similar to that in supervised_learning.py"\rS3keyS\t\t\tS3\t"QIIME test code mapping file, similar to that in supervised_learning.py"\rS3IndexR\t\t\tS3\t"QIIME test code mapping file, similar to that in supervised_learning.py"\rS3ThumbR\t\t\tS3\t"QIIME test code mapping file, similar to that in supervised_learning.py"\rS3MiddleR\t\t\tS3\t"QIIME test code mapping file, similar to that in supervised_learning.py"\rS3keyY\t\t\tS3\t"QIIME test code mapping file, similar to that in supervised_learning.py"\rS3ThumbL\t\t\tS3\t"QIIME test code mapping file, similar to that in supervised_learning.py"\rS3keyF\t\t\tS3\t"QIIME test code mapping file, similar to that in supervised_learning.py"\rS3IndexL\t\t\tS3\t"QIIME test code mapping file, similar to that in supervised_learning.py"\rS3keyW\t\t\tS3\t"QIIME test code mapping file, similar to that in supervised_learning.py"\rS3keyQ\t\t\tS3\t"QIIME test code mapping file, similar to that in supervised_learning.py"\rS3keyL\t\t\tS3\t"QIIME test code mapping file, similar to that in supervised_learning.py"' +# run unit tests if run from command-line +if __name__ == '__main__': + main() diff --git a/tests/test_distance_matrix_from_mapping.py b/tests/test_distance_matrix_from_mapping.py index c353dbc853..7cd7af4325 100644 --- a/tests/test_distance_matrix_from_mapping.py +++ b/tests/test_distance_matrix_from_mapping.py @@ -10,7 +10,7 @@ "Michael S. Robeson", ] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Antonio Gonzalez Pena" __email__ = "antgonza@gmail.com" diff --git a/tests/test_estimate_observation_richness.py b/tests/test_estimate_observation_richness.py index 068b2347ac..4ebc592b2c 100644 --- a/tests/test_estimate_observation_richness.py +++ b/tests/test_estimate_observation_richness.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2013, The QIIME Project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/tests/test_exclude_seqs_by_blast.py b/tests/test_exclude_seqs_by_blast.py index c5de381349..ccdabb4bb7 100644 --- a/tests/test_exclude_seqs_by_blast.py +++ b/tests/test_exclude_seqs_by_blast.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jesse Zaneveld", "Rob Knight"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jesse Zaneveld" __email__ = "zaneveld@gmail.com" diff --git a/tests/test_extract_barcodes.py b/tests/test_extract_barcodes.py index 3604610106..111696eabf 100644 --- a/tests/test_extract_barcodes.py +++ b/tests/test_extract_barcodes.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" # consider project name __credits__ = ["William Walters", "Daniel McDonald"] # remember to add yourself __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Walters" __email__ = "william.a.walters@colorado.edu" diff --git a/tests/test_filter.py b/tests/test_filter.py index 46a04ed43a..3792ad4ec5 100755 --- a/tests/test_filter.py +++ b/tests/test_filter.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_filter_alignment.py b/tests/test_filter_alignment.py index 22e5e7a209..c81ea8932d 100755 --- a/tests/test_filter_alignment.py +++ b/tests/test_filter_alignment.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Dan Knights"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_filter_otus_by_sample.py b/tests/test_filter_otus_by_sample.py index 4622c42941..67d160ae3d 100644 --- a/tests/test_filter_otus_by_sample.py +++ b/tests/test_filter_otus_by_sample.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" # consider project name __credits__ = ["Jesse Stombaugh"] # remember to add yourself __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/tests/test_format.py b/tests/test_format.py index 91a16d980c..8f1f95971f 100755 --- a/tests/test_format.py +++ b/tests/test_format.py @@ -9,7 +9,7 @@ "Jai Ram Rideout", "Jose Antonio Navas Molina"] # remember to add yourself if you make changes __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_golay.py b/tests/test_golay.py index fca20e6ffc..a61bdc4c3e 100644 --- a/tests/test_golay.py +++ b/tests/test_golay.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski", "Rob Knight"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_group.py b/tests/test_group.py index 9feb2e3ab8..c7f3400446 100755 --- a/tests/test_group.py +++ b/tests/test_group.py @@ -8,7 +8,7 @@ "Greg Caporaso", "Jeremy Widmann"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/tests/test_hamming.py b/tests/test_hamming.py index 6840e2c4de..bb97bb4b26 100755 --- a/tests/test_hamming.py +++ b/tests/test_hamming.py @@ -10,7 +10,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" # consider project name __credits__ = ["Micah Hamady", "Rob Knight"] # remember to add yourself __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_hierarchical_cluster.py b/tests/test_hierarchical_cluster.py index 6bffa68908..da8b19a7b8 100644 --- a/tests/test_hierarchical_cluster.py +++ b/tests/test_hierarchical_cluster.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["justin kuczynski"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_identify_chimeric_seqs.py b/tests/test_identify_chimeric_seqs.py index 69d0f4c745..5c35e2b26d 100755 --- a/tests/test_identify_chimeric_seqs.py +++ b/tests/test_identify_chimeric_seqs.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jens Reeder", "William Walters"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_join_paired_ends.py b/tests/test_join_paired_ends.py index 8ddde33420..f77d3f02c1 100644 --- a/tests/test_join_paired_ends.py +++ b/tests/test_join_paired_ends.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2013, The QIIME Project" __credits__ = ["Mike Robeson"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Mike Robeson" __email__ = "robesonms@ornl.gov" diff --git a/tests/test_make_2d_plots.py b/tests/test_make_2d_plots.py index d2be471d43..c104dddcc6 100644 --- a/tests/test_make_2d_plots.py +++ b/tests/test_make_2d_plots.py @@ -6,7 +6,7 @@ # remember to add yourself __credits__ = ["Jesse Stombaugh", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/tests/test_make_bipartite_network.py b/tests/test_make_bipartite_network.py index e1097b3fd5..8dc48376f5 100755 --- a/tests/test_make_bipartite_network.py +++ b/tests/test_make_bipartite_network.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2013, The QIIME project" __credits__ = ["Will Van Treuren"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Will Van Treuren" __email__ = "wdwvt1@gmail.com" diff --git a/tests/test_make_bootstrapped_tree.py b/tests/test_make_bootstrapped_tree.py index 04b9e614bf..013d1571cb 100644 --- a/tests/test_make_bootstrapped_tree.py +++ b/tests/test_make_bootstrapped_tree.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["justin kuczynski"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_make_distance_boxplots.py b/tests/test_make_distance_boxplots.py index ae5825d1c7..c0bd5aeb2d 100644 --- a/tests/test_make_distance_boxplots.py +++ b/tests/test_make_distance_boxplots.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2012, The QIIME project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/tests/test_make_fastq.py b/tests/test_make_fastq.py index 650144d9f8..83fdd9c796 100644 --- a/tests/test_make_fastq.py +++ b/tests/test_make_fastq.py @@ -9,7 +9,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" # consider project name __credits__ = ["Rob Knight"] # remember to add yourself if you make changes __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/tests/test_make_library_id_lists.py b/tests/test_make_library_id_lists.py index 3cf7b3df2d..efd8231fee 100644 --- a/tests/test_make_library_id_lists.py +++ b/tests/test_make_library_id_lists.py @@ -8,7 +8,7 @@ # remember to add yourself if you make changes __credits__ = ["Rob Knight"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/tests/test_make_otu_heatmap.py b/tests/test_make_otu_heatmap.py index 5f80c57ec6..5d1a425665 100644 --- a/tests/test_make_otu_heatmap.py +++ b/tests/test_make_otu_heatmap.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Dan Knights"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Dan Knights" __email__ = "daniel.knights@colorado.edu" diff --git a/tests/test_make_otu_network.py b/tests/test_make_otu_network.py index 962b6e71db..8b836009c1 100644 --- a/tests/test_make_otu_network.py +++ b/tests/test_make_otu_network.py @@ -6,7 +6,7 @@ # remember to add yourself __credits__ = ["Julia Goodrich", "Jose Carlos Clemente Litran"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jose Clemente" __email__ = "jose.clemente@gmail.com" diff --git a/tests/test_make_otu_table.py b/tests/test_make_otu_table.py index 4b3d940e6c..4445628ceb 100644 --- a/tests/test_make_otu_table.py +++ b/tests/test_make_otu_table.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" # consider project name __credits__ = ["Rob Knight", "Justin Kuczynski", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_make_per_library_sff.py b/tests/test_make_per_library_sff.py index 3fa02583e8..5229134b63 100644 --- a/tests/test_make_per_library_sff.py +++ b/tests/test_make_per_library_sff.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Kyle Bittinger"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/tests/test_make_phylogeny.py b/tests/test_make_phylogeny.py index a0c3325b7d..fdb5d03e6f 100644 --- a/tests/test_make_phylogeny.py +++ b/tests/test_make_phylogeny.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Rob Knight"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_make_rarefaction_plots.py b/tests/test_make_rarefaction_plots.py index 120f78f0ce..aa16e6da1e 100755 --- a/tests/test_make_rarefaction_plots.py +++ b/tests/test_make_rarefaction_plots.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jesse Stombaugh", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/tests/test_map_reads_to_reference.py b/tests/test_map_reads_to_reference.py index bbca099317..a951d5bf48 100755 --- a/tests/test_map_reads_to_reference.py +++ b/tests/test_map_reads_to_reference.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_normalize_table.py b/tests/test_normalize_table.py new file mode 100644 index 0000000000..412a760011 --- /dev/null +++ b/tests/test_normalize_table.py @@ -0,0 +1,113 @@ +#!/usr/bin/env python + +from os import close +from tempfile import mkstemp + +from unittest import TestCase, main +from biom import load_table + +from skbio.util import remove_files +from qiime.normalize_table import normalize_CSS, normalize_DESeq +from qiime.util import load_qiime_config +from numpy.testing import assert_almost_equal + + +__author__ = "Sophie Weiss" +__copyright__ = "Copyright 2014, The QIIME Project" +__credits__ = ["Sophie Weiss"] +__license__ = "GPL" +__version__ = "1.9.0-rc1" +__maintainer__ = "Sophie Weiss" +__email__ = "sophie.sjw@gmail.com" + +"""Contains tests for producing CSS and DESeq normalized tables.""" + + + + +class RNormalizeTableTests(TestCase): + + """Tests of the RNormalizeTable class""" + + def setUp(self): + self.qiime_config = load_qiime_config() + self.tmp_dir = self.qiime_config['temp_dir'] or '/tmp/' + + #Temporary input file + fd, self.tmp_otu_fp = mkstemp(dir= self.tmp_dir, + prefix='R_test_otu_table_', + suffix='.biom') + close(fd) + seq_file = open(self.tmp_otu_fp, 'w') + seq_file.write(test_otu_table) + seq_file.close() + + self.tmp_otu_fp_out_CSS = '%s/R_test_otu_table_out_CSS.biom' % (str(self.tmp_dir)) + self.tmp_otu_fp_out_DESeq = '%s/R_test_otu_table_out_DESeq.biom' % (str(self.tmp_dir)) + + self.files_to_remove = \ + [self.tmp_otu_fp, self.tmp_otu_fp_out_CSS, self.tmp_otu_fp_out_DESeq] + + normalize_CSS(self.tmp_otu_fp, self.tmp_otu_fp_out_CSS, output_CSS_statistics=False) + normalize_DESeq(self.tmp_otu_fp, self.tmp_otu_fp_out_DESeq, DESeq_negatives_to_zero=False) + + + def test_normalize_table_CSS(self): + """OTU table IDs should be the same before and after CSS normalization + """ + q=load_table(self.tmp_otu_fp) + self.assertItemsEqual( + q.ids(), + load_table(self.tmp_otu_fp_out_CSS).ids()) + + #test taxonomy added to CSS; DESeq gives negatives so no taxonomy added + # self.assertItemsEqual( + # q._observation_metadata, + # load_table(self.tmp_otu_fp_out_CSS)._observation_metadata) + + """catch any R/metagenomeSeq version changes by testing output against current version + """ + z = load_table(self.tmp_otu_fp_out_CSS) + OTU_1848 = [val[28] for (val, otu_id, meta) in z.iter(axis='sample')] + OTU_1848_CSS = [13.873, 14.185, 13.532, 12.824, 14.666, 14.257, 14.416, 14.993, 13.882, 13.453, 14.84, 14.435, 8.8397, 9.8069, 8.0537, 10.571, 8.3851, 8.27, 6.6582, 8.8221, 11.136, 10.928, 11.419, 9.1489, 9.6962, 14.257, 13.901, 13.288, 13.162, 13.84, 12.759, 13.796, 14.489, 15.433, 13.804, 14.298, 13.484, 14.101] + assert_almost_equal(OTU_1848, OTU_1848_CSS, decimal=3, + err_msg='possible CSS method change, or version change') + + OTU_88 = [val[0] for (val, otu_id, meta) in z.iter(axis='sample')] + OTU_88_CSS = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 5.745, 6.8905, 6.3399, 0.0, 6.8628, 7.0697, 6.6114, 0.0, 0.0, 5.745, 7.3895, 6.4382, 8.7468, 6.6582, 6.1785, 6.398, 6.8088, 7.1685, 6.8088, 0.0, 0.0, 0.0, 7.1685, 0.0, 7.1685] + assert_almost_equal(OTU_88, OTU_88_CSS, decimal=2, + err_msg='possible CSS method change, or version change') + + + def test_normalize_table_DESeq(self): + """OTU table IDs should be the same before and after DESeq normalization + """ + z = load_table(self.tmp_otu_fp_out_DESeq) + self.assertItemsEqual( + load_table(self.tmp_otu_fp).ids(), + z.ids()) + + """catch any R/DESeq version changes by testing output against current version + """ + OTU_1848 = [val[28] for (val, otu_id, meta) in z.iter(axis='sample')] + OTU_1848_DESeq = [7.4334, 7.4437, 7.4609, 6.172, 7.4844, 7.3088, 7.4484, 7.5416, 7.447, 7.4819, 7.6865, 7.5209, 3.1861, 3.7992, 2.6914, 5.1891, 2.9709, 3.3051, 1.3145, 4.0617, 5.8195, 5.194, 5.9127, 3.4936, 4.6303, 7.3194, 7.4484, 7.3309, 7.016, 7.2469, 6.847, 7.2242, 7.5226, 7.7103, 7.3645, 7.3462, 7.1957, 7.1643] + assert_almost_equal(OTU_1848, OTU_1848_DESeq, decimal=3, + err_msg='possible DESeq method change, or version change') + + OTU_88 = [val[0] for (val, otu_id, meta) in z.iter(axis='sample')] + OTU_88_DESeq = [0.28477, 0.30354, 0.27808, 0.28967, 0.28477, 0.27808, 0.27408, 0.28477, 0.28967, 0.27408, 0.32945, 0.32945, -0.56644, 0.6423, 1.7223, 1.5033, 0.20445, 2.207, 1.6455, 2.2115, 0.068394, -0.001519, 1.1843, 1.9803, 1.7614, 2.3137, 1.2806, 1.2782, 1.2782, 1.2697, 1.8815, 1.2896, 0.28188, 0.34588, 0.27808, 1.2852, 0.27408, 1.2806] + assert_almost_equal(OTU_88, OTU_88_DESeq, decimal=3, + err_msg='possible DESeq method change, or version change') + + + def tearDown(self): + """cleanup temporary files and dirs + """ + remove_files(set(self.files_to_remove)) + + +test_otu_table = """{"rows": [{"id": "88", "metadata": {"taxonomy": ["Aa", "other"]}}, {"id": "131", "metadata": {"taxonomy": ["Ab", "other"]}}, {"id": "144", "metadata": {"taxonomy": ["Ac", "other"]}}, {"id": "158", "metadata": {"taxonomy": ["Ad", "other"]}}, {"id": "193", "metadata": {"taxonomy": ["Ae", "other"]}}, {"id": "225", "metadata": {"taxonomy": ["Af", "other"]}}, {"id": "260", "metadata": {"taxonomy": ["Ag", "other"]}}, {"id": "588", "metadata": {"taxonomy": ["Ah", "other"]}}, {"id": "634", "metadata": {"taxonomy": ["Ai", "other"]}}, {"id": "721", "metadata": {"taxonomy": ["Aj", "other"]}}, {"id": "821", "metadata": {"taxonomy": ["Ak", "other"]}}, {"id": "843", "metadata": {"taxonomy": ["Al", "other"]}}, {"id": "883", "metadata": {"taxonomy": ["Am", "other"]}}, {"id": "891", "metadata": {"taxonomy": ["An", "other"]}}, {"id": "976", "metadata": {"taxonomy": ["Ao", "other"]}}, {"id": "979", "metadata": {"taxonomy": ["Ap", "other"]}}, {"id": "983", "metadata": {"taxonomy": ["Aq", "other"]}}, {"id": "1035", "metadata": {"taxonomy": ["Ar", "other"]}}, {"id": "1088", "metadata": {"taxonomy": ["As", "other"]}}, {"id": "1156", "metadata": {"taxonomy": ["At", "other"]}}, {"id": "1287", "metadata": {"taxonomy": ["Au", "other"]}}, {"id": "1314", "metadata": {"taxonomy": ["Av", "other"]}}, {"id": "1351", "metadata": {"taxonomy": ["Aw", "other"]}}, {"id": "1373", "metadata": {"taxonomy": ["Ax", "other"]}}, {"id": "1487", "metadata": {"taxonomy": ["Ay", "other"]}}, {"id": "1582", "metadata": {"taxonomy": ["Az", "other"]}}, {"id": "1591", "metadata": {"taxonomy": ["Ba", "other"]}}, {"id": "1784", "metadata": {"taxonomy": ["Bb", "other"]}}, {"id": "1848", "metadata": {"taxonomy": ["Bc", "other"]}}, {"id": "1886", "metadata": {"taxonomy": ["Bd", "other"]}}, {"id": "2007", "metadata": {"taxonomy": ["Be", "other"]}}, {"id": "2059", "metadata": {"taxonomy": ["Bf", "other"]}}, {"id": "2096", "metadata": {"taxonomy": ["Bg", "other"]}}, {"id": "2187", "metadata": {"taxonomy": ["Bh", "other"]}}, {"id": "2218", "metadata": {"taxonomy": ["Bi", "other"]}}, {"id": "2270", "metadata": {"taxonomy": ["Bj", "other"]}}, {"id": "2328", "metadata": {"taxonomy": ["Bk", "other"]}}, {"id": "2360", "metadata": {"taxonomy": ["Bl", "other"]}}, {"id": "2366", 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8.0], [44, 8, 2.0], [44, 9, 5.0], [44, 10, 1.0], [44, 12, 18.0], [44, 13, 13.0], [44, 14, 12.0], [44, 15, 39.0], [44, 16, 13.0], [44, 17, 4.0], [44, 18, 16.0], [44, 19, 2.0], [44, 20, 32.0], [44, 21, 21.0], [44, 22, 32.0], [44, 23, 13.0], [44, 24, 8.0], [44, 25, 1.0], [44, 27, 2.0], [44, 29, 1.0], [44, 30, 5.0], [44, 32, 3.0], [44, 34, 3.0], [44, 35, 3.0], [44, 36, 3.0], [45, 0, 1.0], [45, 2, 1.0], [45, 3, 1.0], [45, 6, 1.0], [45, 7, 1.0], [45, 9, 2.0], [45, 10, 1.0], [45, 12, 1.0], [45, 13, 1.0], [45, 15, 3.0], [45, 18, 1.0], [45, 22, 2.0], [45, 24, 2.0], [45, 25, 1.0], [45, 30, 2.0], [45, 35, 1.0], [46, 4, 1.0], [46, 12, 2.0], [46, 13, 2.0], [46, 14, 3.0], [46, 15, 3.0], [46, 16, 3.0], [46, 17, 19.0], [46, 18, 3.0], [46, 19, 9.0], [46, 21, 1.0], [46, 22, 2.0], [46, 23, 5.0], [46, 24, 4.0], [46, 26, 1.0], [46, 31, 3.0], [47, 13, 1.0], [47, 14, 1.0], [47, 16, 7.0], [47, 17, 1.0], [47, 18, 1.0], [47, 21, 2.0], [48, 12, 3.0], [48, 14, 3.0], [48, 16, 3.0], [48, 19, 1.0], [48, 21, 1.0], [48, 23, 1.0], [49, 25, 1.0], [49, 26, 1.0], [49, 28, 2.0], [49, 29, 1.0], [49, 30, 2.0], [49, 35, 1.0]], "columns": [{"id": "S1RingL", "metadata": null}, {"id": "S1keyM", "metadata": null}, {"id": "S1keySpace", "metadata": null}, {"id": "S1IndexL", "metadata": null}, {"id": "S1keyK", "metadata": null}, {"id": "S1ThumbR", "metadata": null}, {"id": "S1keyV", "metadata": null}, {"id": "S1IndexR", "metadata": null}, {"id": "S1keyA", "metadata": null}, {"id": "S1RingR", "metadata": null}, {"id": "S1MiddleR", "metadata": null}, {"id": "S1keyD", "metadata": null}, {"id": "S2keySpace", "metadata": null}, {"id": "S2keyJ", "metadata": null}, {"id": "S2keyLeftShift", "metadata": null}, {"id": "S2keyN", "metadata": null}, {"id": "S2keyZ", "metadata": null}, {"id": "S2IndexL", "metadata": null}, {"id": "S2keyA", "metadata": null}, {"id": "S2PinkyL", "metadata": null}, {"id": "S2keyK", "metadata": null}, {"id": "S2keyRightShift", "metadata": null}, {"id": "S2keyM", "metadata": null}, {"id": "S2keyI", "metadata": null}, {"id": "S2PinkyR", "metadata": null}, {"id": "S3keySpace", "metadata": null}, {"id": "S3keyEnter", "metadata": null}, {"id": "S3keyS", "metadata": null}, {"id": "S3IndexR", "metadata": null}, {"id": "S3ThumbR", "metadata": null}, {"id": "S3MiddleR", "metadata": null}, {"id": "S3keyY", "metadata": null}, {"id": "S3ThumbL", "metadata": null}, {"id": "S3keyF", "metadata": null}, {"id": "S3IndexL", "metadata": null}, {"id": "S3keyW", "metadata": null}, {"id": "S3keyQ", "metadata": null}, {"id": "S3keyL", "metadata": null}], "generated_by": "QIIME 1.4.0-dev, svn revision 2595", "matrix_type": "sparse", "shape": [50, 38], "format_url": "http://www.qiime.org/svn_documentation/documentation/biom_format.html", "date": "2011-12-22T01:46:08.091846", "type": "OTU table", "id": null, "matrix_element_type": "float"}""" + +# run unit tests if run from command-line +if __name__ == '__main__': + main() \ No newline at end of file diff --git a/tests/test_otu_significance.py b/tests/test_otu_significance.py index 0a2b3b5a3c..65964af27f 100755 --- a/tests/test_otu_significance.py +++ b/tests/test_otu_significance.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2013, The QIIME project" __credits__ = ["Luke Ursell", "Will Van Treuren", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Luke Ursell" __email__ = "lkursell@gmail.com" diff --git a/tests/test_parallel/test_align_seqs.py b/tests/test_parallel/test_align_seqs.py index 97938718c8..3b73c35a7f 100755 --- a/tests/test_parallel/test_align_seqs.py +++ b/tests/test_parallel/test_align_seqs.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_parallel/test_alpha_diversity.py b/tests/test_parallel/test_alpha_diversity.py index ac337064bc..aeac617166 100755 --- a/tests/test_parallel/test_alpha_diversity.py +++ b/tests/test_parallel/test_alpha_diversity.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_parallel/test_assign_taxonomy.py b/tests/test_parallel/test_assign_taxonomy.py index 19e227ccb0..cdb0dcfcf7 100755 --- a/tests/test_parallel/test_assign_taxonomy.py +++ b/tests/test_parallel/test_assign_taxonomy.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2012, The QIIME project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/tests/test_parallel/test_beta_diversity.py b/tests/test_parallel/test_beta_diversity.py index d0e7c06aea..9985221494 100755 --- a/tests/test_parallel/test_beta_diversity.py +++ b/tests/test_parallel/test_beta_diversity.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_parallel/test_blast.py b/tests/test_parallel/test_blast.py index 61b81dccd9..33efc305d2 100755 --- a/tests/test_parallel/test_blast.py +++ b/tests/test_parallel/test_blast.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2012, The QIIME project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/tests/test_parallel/test_identify_chimeric_seqs.py b/tests/test_parallel/test_identify_chimeric_seqs.py index d43e22a611..b8c811683d 100755 --- a/tests/test_parallel/test_identify_chimeric_seqs.py +++ b/tests/test_parallel/test_identify_chimeric_seqs.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2012, The QIIME project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/tests/test_parallel/test_map_reads_to_reference.py b/tests/test_parallel/test_map_reads_to_reference.py index dd36554501..c50e3eb412 100755 --- a/tests/test_parallel/test_map_reads_to_reference.py +++ b/tests/test_parallel/test_map_reads_to_reference.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_parallel/test_merge_otus.py b/tests/test_parallel/test_merge_otus.py index cf9a09ad61..904252ba85 100644 --- a/tests/test_parallel/test_merge_otus.py +++ b/tests/test_parallel/test_merge_otus.py @@ -10,7 +10,7 @@ __copyright__ = "Copyright 2013, The QIIME Project" __credits__ = ["Daniel McDonald", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Daniel McDonald" __email__ = "mcdonadt@colorado.edu" diff --git a/tests/test_parallel/test_multiple_rarefactions.py b/tests/test_parallel/test_multiple_rarefactions.py index bfa7407944..50eb6c8c49 100755 --- a/tests/test_parallel/test_multiple_rarefactions.py +++ b/tests/test_parallel/test_multiple_rarefactions.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_parallel/test_pick_otus.py b/tests/test_parallel/test_pick_otus.py index 46b2bd0054..3adbbfb335 100755 --- a/tests/test_parallel/test_pick_otus.py +++ b/tests/test_parallel/test_pick_otus.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Jens Reeder"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_parallel/test_util.py b/tests/test_parallel/test_util.py index eba9fc6a05..492b02b703 100755 --- a/tests/test_parallel/test_util.py +++ b/tests/test_parallel/test_util.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_parse.py b/tests/test_parse.py index 7a76c21cf6..4da35b2189 100644 --- a/tests/test_parse.py +++ b/tests/test_parse.py @@ -8,7 +8,7 @@ "Jai Ram Rideout", "Will Van Treuren", "Yoshiki Vazquez-Baeza", "Jose Antonio Navas Molina"] # remember to add yourself __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_pick_otus.py b/tests/test_pick_otus.py index e001cc03dd..bbddc8bb3d 100755 --- a/tests/test_pick_otus.py +++ b/tests/test_pick_otus.py @@ -13,7 +13,7 @@ "William Walters", "Jose Carlos Clemente Litran"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_pick_rep_set.py b/tests/test_pick_rep_set.py index a4a4596fbe..4a3e1486fb 100644 --- a/tests/test_pick_rep_set.py +++ b/tests/test_pick_rep_set.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Rob Knight", "Kyle Bittinger", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Daniel McDonald" __email__ = "wasade@gmail.com" diff --git a/tests/test_plot_rank_abundance_graph.py b/tests/test_plot_rank_abundance_graph.py index c913c0b4c4..20ab3dd120 100755 --- a/tests/test_plot_rank_abundance_graph.py +++ b/tests/test_plot_rank_abundance_graph.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jens Reeder", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_plot_semivariogram.py b/tests/test_plot_semivariogram.py index f0b70349f0..e3878a06dd 100644 --- a/tests/test_plot_semivariogram.py +++ b/tests/test_plot_semivariogram.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Antonio Gonzalez Pena"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Antonio Gonzalez Pena" __email__ = "antgonza@gmail.com" diff --git a/tests/test_plot_taxa_summary.py b/tests/test_plot_taxa_summary.py index 69722eb229..5bcd5496f1 100644 --- a/tests/test_plot_taxa_summary.py +++ b/tests/test_plot_taxa_summary.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" # consider project name __credits__ = ["Jesse Stombaugh", "Julia Goodrich"] # remember to add yourself __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/tests/test_principal_coordinates.py b/tests/test_principal_coordinates.py index 6242d985e7..7739e60143 100644 --- a/tests/test_principal_coordinates.py +++ b/tests/test_principal_coordinates.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_process_sff.py b/tests/test_process_sff.py index c4838a40b6..4b2c529cd9 100644 --- a/tests/test_process_sff.py +++ b/tests/test_process_sff.py @@ -25,7 +25,7 @@ "Jesse Stombaugh", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/tests/test_quality_scores_plot.py b/tests/test_quality_scores_plot.py index ea36258fc3..407ee385d0 100755 --- a/tests/test_quality_scores_plot.py +++ b/tests/test_quality_scores_plot.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/tests/test_rarefaction.py b/tests/test_rarefaction.py index ca5cbe22ea..0b34eafb9b 100644 --- a/tests/test_rarefaction.py +++ b/tests/test_rarefaction.py @@ -5,7 +5,7 @@ __credits__ = ["justin kuczynski", "Rob Knight", "Jose Carlos Clemente Litran", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_relatedness.py b/tests/test_relatedness.py index ccda023cd5..03100f5e22 100644 --- a/tests/test_relatedness.py +++ b/tests/test_relatedness.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["William Van Treuren"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Van Treuren" __email__ = "wdwvt1@gmail.com" diff --git a/tests/test_remote.py b/tests/test_remote.py index d78499bba6..e1550fdfd9 100644 --- a/tests/test_remote.py +++ b/tests/test_remote.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2012, The QIIME project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/tests/test_shared_phylotypes.py b/tests/test_shared_phylotypes.py index a4e43d588e..9fdcc06ac6 100644 --- a/tests/test_shared_phylotypes.py +++ b/tests/test_shared_phylotypes.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jens Reeder", "Daniel McDonald"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jose Clemente" __email__ = "jose.clemente@gmail.com" diff --git a/tests/test_simsam.py b/tests/test_simsam.py index ca1a8abb87..73e6793038 100755 --- a/tests/test_simsam.py +++ b/tests/test_simsam.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kucyznski", "Jai Ram Rideout", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kucyznski" __email__ = "justinak@gmail.com" diff --git a/tests/test_sort.py b/tests/test_sort.py index d08c9a0e7c..7d9737ff48 100755 --- a/tests/test_sort.py +++ b/tests/test_sort.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Daniel McDonald", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_split.py b/tests/test_split.py index cf7c767245..9c02a17bb8 100755 --- a/tests/test_split.py +++ b/tests/test_split.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Will Van Treuren"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_split_libraries.py b/tests/test_split_libraries.py index 6ab1141b9c..e250f832e8 100644 --- a/tests/test_split_libraries.py +++ b/tests/test_split_libraries.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Rob Knight", "William Walters", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Walters" __email__ = "william.a.walters@colorado.edu" diff --git a/tests/test_split_libraries_fastq.py b/tests/test_split_libraries_fastq.py index 98c3c27230..6c70aef52a 100755 --- a/tests/test_split_libraries_fastq.py +++ b/tests/test_split_libraries_fastq.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Jose Antonio Navas Molina", "Daniel McDonald"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_split_libraries_lea_seq.py b/tests/test_split_libraries_lea_seq.py index d07c68e14a..8b45b590c2 100644 --- a/tests/test_split_libraries_lea_seq.py +++ b/tests/test_split_libraries_lea_seq.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2014, The QIIME Project" __credits__ = ["Charudatta Navare"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Charudatta Navare" __email__ = "charudatta.navare@gmail.com" diff --git a/tests/test_stats.py b/tests/test_stats.py index 5af2c2623f..159b3cb9ee 100644 --- a/tests/test_stats.py +++ b/tests/test_stats.py @@ -7,7 +7,7 @@ "Damien Coy", "Levi McCracken", "Andrew Cochran", "Will Van Treuren"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/tests/test_summarize_taxa.py b/tests/test_summarize_taxa.py index 207d01e6dc..d8619fbde5 100644 --- a/tests/test_summarize_taxa.py +++ b/tests/test_summarize_taxa.py @@ -11,7 +11,7 @@ "Antonio Gonzalez Pena", "Jose Carlos Clemente Litran"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Daniel McDonald" __email__ = "wasade@gmail.com" diff --git a/tests/test_supervised_learning.py b/tests/test_supervised_learning.py index 8db5acf02b..b04e08bb7a 100644 --- a/tests/test_supervised_learning.py +++ b/tests/test_supervised_learning.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Dan Knights", "Luke Ursell"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Dan Knights" __email__ = "daniel.knights@colorado.edu" diff --git a/tests/test_transform_coordinate_matrices.py b/tests/test_transform_coordinate_matrices.py index 941630c6e8..aebceda5ee 100755 --- a/tests/test_transform_coordinate_matrices.py +++ b/tests/test_transform_coordinate_matrices.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_tree_compare.py b/tests/test_tree_compare.py index f5965cd433..cd2d728c0a 100644 --- a/tests/test_tree_compare.py +++ b/tests/test_tree_compare.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski", "Daniel McDonald"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_trim_sff_primers.py b/tests/test_trim_sff_primers.py index 133ccb4d98..f91bd7bb40 100644 --- a/tests/test_trim_sff_primers.py +++ b/tests/test_trim_sff_primers.py @@ -10,7 +10,7 @@ # remember to add yourself if you make changes __credits__ = ["Rob Knight", 'Kyle Bittinger'] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/tests/test_truncate_fasta_qual_files.py b/tests/test_truncate_fasta_qual_files.py index 20921276a4..b016140a8f 100755 --- a/tests/test_truncate_fasta_qual_files.py +++ b/tests/test_truncate_fasta_qual_files.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/tests/test_truncate_reverse_primer.py b/tests/test_truncate_reverse_primer.py index f48483f3b3..1a93a6e10b 100755 --- a/tests/test_truncate_reverse_primer.py +++ b/tests/test_truncate_reverse_primer.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/tests/test_util.py b/tests/test_util.py index 5692b3c26a..437104627c 100755 --- a/tests/test_util.py +++ b/tests/test_util.py @@ -69,7 +69,7 @@ "Levi McCracken", "Damien Coy", "Yoshiki Vazquez Baeza", "Will Van Treuren", "Luke Ursell"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_validate_demultiplexed_fasta.py b/tests/test_validate_demultiplexed_fasta.py index 516cea1a0b..5eba04e882 100755 --- a/tests/test_validate_demultiplexed_fasta.py +++ b/tests/test_validate_demultiplexed_fasta.py @@ -7,7 +7,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Anton Walters"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Anton Walters" __email__ = "william.a.walters@gmail.com" diff --git a/tests/test_validate_mapping_file.py b/tests/test_validate_mapping_file.py index 34fa18ec23..72c44f124b 100755 --- a/tests/test_validate_mapping_file.py +++ b/tests/test_validate_mapping_file.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" # consider project name __credits__ = ["Rob Knight", "William Walters"] # remember to add yourself __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Walters" __email__ = "william.a.walters@colorado.edu" diff --git a/tests/test_workflow/test_ampliconnoise.py b/tests/test_workflow/test_ampliconnoise.py index 218c838c19..838bd3d679 100755 --- a/tests/test_workflow/test_ampliconnoise.py +++ b/tests/test_workflow/test_ampliconnoise.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Kyle Bittinger", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_workflow/test_core_diversity_analyses.py b/tests/test_workflow/test_core_diversity_analyses.py index 0d9be67a7b..357ef2b97d 100755 --- a/tests/test_workflow/test_core_diversity_analyses.py +++ b/tests/test_workflow/test_core_diversity_analyses.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_workflow/test_downstream.py b/tests/test_workflow/test_downstream.py index 89cd81e1df..e8b77d4547 100755 --- a/tests/test_workflow/test_downstream.py +++ b/tests/test_workflow/test_downstream.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Kyle Bittinger", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_workflow/test_pick_open_reference_otus.py b/tests/test_workflow/test_pick_open_reference_otus.py index e9a7844120..feff9d9724 100755 --- a/tests/test_workflow/test_pick_open_reference_otus.py +++ b/tests/test_workflow/test_pick_open_reference_otus.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_workflow/test_preprocess.py b/tests/test_workflow/test_preprocess.py index f264196d4a..8225133219 100755 --- a/tests/test_workflow/test_preprocess.py +++ b/tests/test_workflow/test_preprocess.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/tests/test_workflow/test_upstream.py b/tests/test_workflow/test_upstream.py index 28f93a0d08..a881c247fc 100755 --- a/tests/test_workflow/test_upstream.py +++ b/tests/test_workflow/test_upstream.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Kyle Bittinger", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_workflow/test_util.py b/tests/test_workflow/test_util.py index 8d1231df4d..8c61092ae9 100755 --- a/tests/test_workflow/test_util.py +++ b/tests/test_workflow/test_util.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Kyle Bittinger", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.8.0-dev" +__version__ = "1.9.0-rc1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com"