Merge branch 'master' into master

README.md

@@ -14,6 +14,7 @@ To use with an existing installation please extract and place the mm10 directory
 Upstream and downstream tools (PrepareAA, AmpliconClassifier, CycleViz) are also enabled to accept the `--ref mm10`
 argument. 
 
+
 **[Older update descriptions are available here.](https://docs.google.com/document/d/1jqnCs46hrpYGBGrZQFop31ezskyludxNJEQdZONwFdc/edit?usp=sharing)**
 
 ## Introduction
@@ -46,7 +47,7 @@ AmpliconArchitect was developed by Viral Deshpande, and is maintained by Jens Lu
     * `export MOSEKLM_LICENSE_FILE=<Parent directory of mosek.lic> >> ~/.bashrc && source ~/.bashrc`
 3. Download AA data repositories and set environment variable AA_DATA_REPO:
     * Download from ` https://datasets.genepattern.org/?prefix=data/module_support_files/AmpliconArchitect/`
-    
+
 #### Usage:
 
 `$AA --bam {input_bam} --bed {bed file} --out {prefix_of_output_files} <optional arguments>`
@@ -71,6 +72,7 @@ AA can be installed in 2 ways:
     * `export MOSEKLM_LICENSE_FILE=<Parent directory of mosek.lic> >> ~/.bashrc && source ~/.bashrc`
 3. Download AA data repositories and set environment variable AA_DATA_REPO:
     * Download from ` https://datasets.genepattern.org/?prefix=data/module_support_files/AmpliconArchitect/`
+
     * Set enviroment variable AA_DATA_REPO to point to the data_repo directory:
         ```bash
         mkdir data_repo && cd data_repo
@@ -119,6 +121,7 @@ sudo python2 get-pip.py
 
 
 Note that 0.15.2 is the last version of pysam which appears to support pip2 installation, however AA itself supports the more recent versions.
+
 4. Mosek optimization tool version 8.x (https://www.mosek.com/). **Due to breaking changes in the newer versions of Mosek, we require version 8 to be used**:
 ```bash
 wget http://download.mosek.com/stable/8.0.0.60/mosektoolslinux64x86.tar.bz2
@@ -135,6 +138,7 @@ cd $PWD/mosek/8/tools/platform/linux64x86/python/3/
 # sudo python2 setup.py install #(--user)
 
 sudo python3 setup.py install #(--user) [can also build locally with "pip install -e ."]
+
 cd -
 source ~/.bashrc
 ```
@@ -176,7 +180,7 @@ AA can also be run through Nextflow, using the [nf-core/circdna pipeline](https:
 
 #### PrepareAA:
 We provide a wrapper for jumping off at any intermediate step including generating the prerequisite BAM alignments with BWA, CNV calls for seeding and CNV seed selection. PrepareAA is available at https://github.com/jluebeck/PrepareAA. We recommmend this for users who are less experienced with AA as it greatly simplifies the process of selecting CNV seed regions to feed to AA.
-PrepareAA can directly invoke AA if installed. 
+PrepareAA can directly invoked AA if installed. 
 
 
 ### 1) Input data:
@@ -194,8 +198,9 @@ AA requires 2 input files:
         - CNVs from CNV caller ReadDepth (with parameter file `$AA_SRC/src/read_depth_params`), Canvas and CNVkit
         - Select CNVs with copy number > 5x and size > 100kbp (default) and merge adjacent CNVs into a single interval using:
 
-            `python $AA_SRC/amplified_intervals.py --bed {read_depth_folder}/output/alts.dat --out {outFileNamePrefix} --bam {BamFileName}`
+            `python2 $AA_SRC/amplified_intervals.py --bed {read_depth_folder}/output/alts.dat --out {outFileNamePrefix} --bam {BamFileName} --ref {ref}`
         - ***Note that this preprocessing step is critical to AA as it removes low-mappability and low-complexity regions. 
+        - Optional argument `--ref` should match the name of the folder in `data_repo` which corresponds to the version of human reference genome used in the BAM file.
 
 ### 2) Usage:
 `$AA --bam {input_bam} --bed {bed file} --out {prefix_of_output_files} <optional arguments>`

docker/Dockerfile

@@ -42,6 +42,7 @@ RUN fc-cache -f
 
 RUN pip2 install -r /home/requirements/pip2_requirements.txt
 
+
 RUN cd /home/programs && wget http://download.mosek.com/stable/8.0.0.60/mosektoolslinux64x86.tar.bz2
 RUN cd /home/programs && tar xf mosektoolslinux64x86.tar.bz2
 # ADD mosek.lic /home/programs/mosek/8/licenses/mosek.lic

src/AmpliconArchitect.py

@@ -1,5 +1,6 @@
 #!/usr/bin/env python
 
+
 # This software is Copyright 2017 The Regents of the University of California. All Rights Reserved. Permission to copy, modify, and distribute this software and its documentation for educational, research and non-profit purposes, without fee, and without a written agreement is hereby granted, provided that the above copyright notice, this paragraph and the following three paragraphs appear in all copies. Permission to make commercial use of this software may be obtained by contacting:
 #
 # Office of Innovation and Commercialization
@@ -42,7 +43,6 @@
 else:
     from cStringIO import StringIO
 
-
 import global_names
 
 __version__ = "1.3_r1"
@@ -188,6 +188,7 @@ def process(self, msg, kwargs):
 else:
     logging.debug("#TIME " + '%.3f\t'%(time() - TSTART) + "cstats not found, generating coverage statistics... ")
 
+
 coverage_windows=None
 if cbed is not None:
     coverage_windows=hg.interval_list(cbed, 'bed')

src/amplified_intervals.py

@@ -35,6 +35,7 @@
 GAIN = 4.5
 CNSIZE_MIN = 50000
 
+
 parser = argparse. \
     ArgumentParser(description="Filter and merge amplified intervals")
 parser.add_argument('--bed', dest='bed',
@@ -111,6 +112,7 @@
 
         coverage_stats_file.close()
 
+
     bamFileb2b = b2b.bam_to_breakpoint(bamFile, coverage_stats=cstats)
     pre_int_list = []
     for r in rdList:

src/bam_to_breakpoint.py

@@ -1037,6 +1037,7 @@ def edge_has_high_entropy(self, read_list):
             bp2_entropy = max([stats.entropy(np.unique([x for x in rr[1].query_alignment_sequence.upper() if x != 'N'], return_counts=True)[1]) for rr in read_list])
 
         logging.debug("#TIME " + '%.3f\t'%(time() - TSTART) + " breakpoint_entropy: %.3f %.3f" % (bp1_entropy, bp2_entropy))
+
         if bp1_entropy < self.breakpoint_entropy_cutoff:
             return False
         if bp2_entropy < self.breakpoint_entropy_cutoff: