Edited code documentation

README.rst

@@ -1,4 +1,4 @@
-ITSxpress: Software to rapidly trim  the Internally transcribed spacer (ITS) region of FASTQ files 
+ITSxpress: Software to rapidly trim  the Internally transcribed spacer (ITS) region of FASTQ files
 ==================================================================================================
 .. image:: https://travis-ci.org/USDA-ARS-GBRU/itsxpress.svg?branch=master
     :target: https://travis-ci.org/USDA-ARS-GBRU/itsxpress
@@ -9,6 +9,9 @@ ITSxpress: Software to rapidly trim  the Internally transcribed spacer (ITS) reg
 .. image:: https://api.codacy.com/project/badge/Grade/7e2a4c97cde74bccb3e84b706d7a2aa5
   :target: https://www.codacy.com/app/GBRU/itsxpress?utm_source=github.com&utm_medium=referral&utm_content=USDA-ARS-GBRU/itsxpress&utm_campaign=Badge_Grade
 
+.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1304349.svg
+  :target: https://doi.org/10.5281/zenodo.1304349
+
 Author
 -------
 * Adam R. Rivers, US Department of Agriculture, Agricultural Research Service
@@ -19,7 +22,7 @@ Introduction
 
 The internally transcribed spacer region is a region between highly conserved the small
 subunit (SSU) of rRNA and the large subunit (LSU) of the rRNA. In Eukaryotes it contains
-the 5.8s genes and two variable length spacer regions. In amplicon sequening studies it is
+the 5.8s genes and two variable length spacer regions. In amplicon sequencing studies it is
 common practice to trim off the conserved (SSU, 5,8S or LSU) regions. `Bengtsson-Palme
 et al. (2013)`_ published software the software package ITSx_ to do this.
 
@@ -29,25 +32,27 @@ sequence, so each input sequence must be trimmed. ITSXpress makes this possible
 taking FASTQ data, de-replicating the sequences then identifying the start and stop
 sites using HMMSearch.  Results are parsed and the trimmed files are returned. The ITS 1,
 ITS2 or the entire ITS region including the 5.8s rRNA gene can be selected. ITSxpress
-uses the hmm model from ITSx so results are comprable.
+uses the hmm model from ITSx so results are comparable.
 
+ITSxpress is also available as a `QIIME2 Plugin`_
 
-.. _`Bengtsson-Palme et al. (2013)`: https://doi.org/10.1111/2041-210X.12073 
+.. _`Bengtsson-Palme et al. (2013)`: https://doi.org/10.1111/2041-210X.12073
 .. _ITSx: http://microbiology.se/software/itsx/
 .. _OTUs: https://doi.org/10.1038/ismej.2017.119
+.. _`QIIME2 Plugin`: https://github.com/USDA-ARS-GBRU/q2_itsxpress
 
 
 Installation
 -------------
 ITSxpress can be installed from:
 
-1. Preferred method - Bioconda (to be done):
+1. Bioconda: (preferred method because it handles dependencies):
 
 .. code-block:: bash
 
     conda install itsxpress
 
-2. Pip: 
+2. Pip: https://pypi.org/project/itsxpress/:
 
 .. code-block:: bash
 
@@ -63,91 +68,91 @@ ITSxpress can be installed from:
 
 Dependencies
 -------------
-The software requires Vsearch, BBtools, Hmmer and Biopython. Bioconda takes care of this
-for you so it is the preferred installation method.
+The software requires Vsearch, BBtools, Hmmer >= 3.1b and Biopython. Bioconda
+takes care of this for you so it is the preferred installation method.
 
 
-Usage 
+Usage
 ---------
 
 -h, --help            	Show this help message and exit.
 
 --fastq 				A ``.fastq``, ``.fq``, ``.fastq.gz`` or ``.fq.gz`` file. Interleaved
-                        	or not.
-                        
---single_end 			A flag to specify if the fastq file is inteleaved.
+                        	or not. Required.
+
+--single_end 			A flag to specify that the fastq file is single-ended (not paired).
                         	single-ended (not paired). Default is false.
-
---fastq2 				A ``.fastq``, ``.fq``, ``.fastq.gz`` or ``.fq.gz`` file representing read 2, optional.
 
---outfile				The trimmed Fastq file, if it ends in ``gz`` it will be gzipped.
+--fastq2 				A ``.fastq``, ``.fq``, ``.fastq.gz`` or ``.fq.gz`` file representing read 2 if present, optional.
 
---tempdir				Specify the temp file directory.
+--outfile				The trimmed FASTQ file, if it ends in ``gz`` it will be gzipped.
 
---keeptemp				Should intermediate files be kept?
+--tempdir				Specify the temp file directory. Default is None.
+
+--keeptemp				Should intermediate files be kept? Default is false.
 
 --region 				Options : {ITS2, ITS1, ALL}
 
 --taxa					Select the taxonomic group sequenced: {Alveolata, Bryophyta,
 						Bacillariophyta, Amoebozoa, Euglenozoa, Fungi, Chlorophyta,
-						Rhodophyta, Phaeophyceae, Marchantiophyta, Metazoa, Microsporidia,
+						Rhodophyta, Phaeophyceae, Marchantiophyta, Metazoa,
 						Oomycota, Haptophyceae, Raphidophyceae, Rhizaria, Synurophyceae,
-						Tracheophyta, Eustigmatophyceae, Apusozoa, Parabasalia}
-						
---log		          	Log file
+						Tracheophyta, Eustigmatophyceae, All}. Default Fungi.
+
+--log		          	Log file. Default is ITSxpress.log.
 
---threads		     	Number of processor threads to use
+--threads		     	Number of processor threads to use. Default is 1.
 
 
 Examples
 ---------
 
-Use case 1: Trimming the ITS2 region from a fungal amplicon sequencing dataset with 
-forward and reverse gzipped fastq files using two cpu threads.
+Use case 1: Trimming the ITS2 region from a fungal amplicon sequencing dataset with
+forward and reverse gzipped FASTQ files using two cpu threads.
 
 .. code-block:: bash
 
-    itsxpress --fastq r1.fastq.gz --fastq2 r2.fastq.gz --region ITS2 --taxa Fungi \
-    --log logfile.txt --outfile trimmed_reads.fastq.gz --threads 2
+    itsxpress --fastq r1.fastq.gz --fastq2 r2.fastq.gz --region ITS2 \
+    --taxa Fungi --log logfile.txt --outfile trimmed_reads.fastq.gz --threads 2
+
+ITSxpress can take gzipped or un-gzipped FASTQ files and it can write gzipped or
+un-gzipped FASTQ files. It expects FASTQ files to end in: .fq, .fastq, .fq.gz or fastq.gz.
 
-ITSxpress can take gzipped or ungzipped fastq files and it can write gzipped or 
-ungzipped fastq files. It expects fastq files to end in : .fq, .fastq, .fq.gz or fastq.gz
 
+Use case 2: Trimming the ITS2 region from a fungal amplicon sequencing dataset with
+an interleaved gzipped FASTQ files using two cpu threads.
 
-Use case 2: Trimming the ITS2 region from a fungal amplicon sequencing dataset with 
-an interleaved gzipped fastq files using two cpu threads.
-
 .. code-block:: bash
 
     itsxpress --fastq interleaved.fastq.gz  --region ITS2 --taxa Fungi \
     --log logfile.txt --outfile trimmed_reads.fastq.gz --threads 2
 
 
-Use case 3: Trimming the ITS2 region from a fungal amplicon sequencing dataset with 
-an interleaved gzipped fastq files using two cpu threads.
- 
+Use case 3: Trimming the ITS2 region from a fungal amplicon sequencing dataset with
+an single-ended gzipped FASTQ files using two cpu threads.
+
 .. code-block:: bash
 
     itsxpress --fastq single-end.fastq.gz --single_end --region ITS2 --taxa Fungi \
     --log logfile.txt --outfile trimmed_reads.fastq.gz --threads 2
 
-Single ended data is less common and may come from a dataset where the reads have already 
+Single ended data is less common and may come from a dataset where the reads have already
 been merged.
 
-Use case 4: Trimming the ITS1 region from a Microsporidia amplicon sequencing dataset with 
-an interleaved gzipped fastq files using 40 cpu threads.
+Use case 4: Trimming the ITS1 region from a Alveolata amplicon sequencing dataset with
+an interleaved gzipped FASTQ files using 40 cpu threads.
 
 .. code-block:: bash
 
-    itsxpress --fastq interleaved.fastq.gz --region ITS1 --taxa Microsporidia \
+    itsxpress --fastq interleaved.fastq.gz --region ITS1 --taxa Alveolata \
     --log logfile.txt --outfile trimmed_reads.fastq.gz --threads 40
 
 
 License information
 --------------------
 
-This software is a work of the United States Department of Agriculture, Agricultural 
-Research Service. 17 U.S.C. Section 105 states that "Copyright protection under this 
-title is not available for any work of the United States Government".  While I anticipate 
-that this work will be released under a CC0 public domain attribution, only the USDA ARS 
-Office of Technology transfer has the authority to make that determination. 
+This software is a work of the United States Department of Agriculture, Agricultural
+Research Service. 17 U.S.C. Section 105 states that "Copyright protection under this
+title is not available for any work of the United States Government".  While I anticipate
+that this work will be released under a CC0 public domain attribution, only the USDA ARS
+Office of Technology transfer has the authority to make that determination.

itsxpress/definitions.py

@@ -1,3 +1,6 @@
+"""Definitions.py: variables shared across the package.
+
+"""
 import os
 
 # This is the project Root
@@ -36,4 +39,4 @@
  "Rhodophyta":"H.hmm","Phaeophyceae":"I.hmm","Marchantiophyta":"L.hmm","Metazoa":"M.hmm",
  "Oomycota":"O.hmm","Haptophyceae":"P.hmm",
  "Raphidophyceae":"Q.hmm"," Rhizaria":"R.hmm","Synurophyceae":"S.hmm",
- "Tracheophyta":"T.hmm","Eustigmatophyceae":"U.hmm","All":"all.hmm"}
+ "Tracheophyta":"T.hmm","Eustigmatophyceae":"U.hmm","All":"all.hmm"}