| Previous changeset 1:ebe5ec2e244d (2017-09-23) Next changeset 3:4f744d3aaf0b (2017-09-24) |
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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 301fc26e062ac02a28676a05aa9c82e4407e3d29 |
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modified:
probecoverage.xml test-data/graph.pdf |
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added:
multicov.py test-data/coverage_pysam.tab test-data/graph_pysam.pdf |
| b |
| diff -r ebe5ec2e244d -r 35d2db3753d9 multicov.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multicov.py Sun Sep 24 13:34:16 2017 -0400 |
| [ |
| @@ -0,0 +1,60 @@ +import argparse + +import numpy + +import pysam + + +def Parser(): + the_parser = argparse.ArgumentParser() + the_parser.add_argument('-bams', '--bams', dest='bams', required=True, + nargs='+', help='list of input BAM files') + the_parser.add_argument('-bed', '--bed', dest='bed', required=True, + help='Coordinates of probes in a bed file') + args = the_parser.parse_args() + return args + + +def compute_coverage(bam, bed, quality=10): + bam_object = pysam.AlignmentFile(bam, 'rb') + bed_object = open(bed, 'r') + coverage_column = [] + for line in bed_object: + if line[0] == '#': + continue + fields = line[:-1].split('\t') + chr = fields[0] + start = fields[1] + end = fields[2] + coverage = bam_object.count_coverage(reference=chr, + start=int(start)-1, + end=int(end), + quality_threshold=quality) + """ Add the 4 coverage values """ + coverage = [sum(x) for x in zip(*coverage)] + coverage_column.append(numpy.mean(coverage)) + bed_object.close() + return coverage_column + + +def main(bams, bed): + column_dict = {} + for i, bam in enumerate(bams): + column_dict[i] = compute_coverage(bam, bed) + F = open(bed, 'r') + line_counter = 0 + for line in F: + if line[0] == '#': + continue + prefix = line[:-1] + crossline = [] + for col in sorted(column_dict): + crossline.append(str(column_dict[col][line_counter])) + line_counter += 1 + suffix = '\t'.join(crossline) + print('%s\t%s' % (prefix, suffix)) + + +if __name__ == "__main__": + args = Parser() + main(args.bams, args.bed) |
| b |
| diff -r ebe5ec2e244d -r 35d2db3753d9 probecoverage.xml --- a/probecoverage.xml Sat Sep 23 12:56:17 2017 -0400 +++ b/probecoverage.xml Sun Sep 24 13:34:16 2017 -0400 |
| b |
| @@ -1,11 +1,12 @@ -<tool id="probecoverage" name="Probe Coverage" version="0.2.0"> +<tool id="probecoverage" name="Probe Coverage" version="0.3.0"> <description></description> <requirements> <requirement type="package" version="1.4.1">samtools</requirement> <requirement type="package" version="2.26.0">bedtools</requirement> <requirement type="package" version="1.3.2=r3.3.1_0">r-optparse</requirement> <requirement type="package" version="2.2.1=r3.3.1_0">r-ggplot2</requirement> - <requirement type="package" version="1.4.2=r3.3.1_0">r-reshape2</requirement> + <requirement type="package" version="1.11.2=py27_0">numpy</requirement> + <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" description="Tool exception" /> @@ -14,16 +15,25 @@ #for $file in $inputs samtools index '$file' && #end for - bedtools multicov + #if $method == 'pysam': + python $__tool_directory__/multicov.py + #else: + bedtools multicov + #end if -bams #for $file in $inputs '$file' #end for - -bed '$bed' > $bedtools_table && + -bed '$bed' > $coverage_dataframe && Rscript '$__tool_directory__'/probecoverage.r - --input '$bedtools_table' + --input '$coverage_dataframe' --title 'Probe coverage depth (cumulative distribution)' - --xlab 'Depth' + --xlab + #if $method == 'pysam': + 'Depth (pysam method)' + #else: + 'Depth (bedtools muticov method)' + #end if --ylab 'Fraction of covered regions with coverage >= Depth' --output '$distribution' --sample " @@ -33,13 +43,16 @@ " ]]></command> - <inputs> - <param name="inputs" type="data" format="bam" label="Select multiple Bam alignments to parse" multiple="True"/> - <param name="bed" type="data" format="bed" label="Select a bed file describing the genomic regions to analyze" /> - </inputs> +<inputs> + <param name="inputs" type="data" format="bam" label="Select multiple Bam alignments to parse" multiple="True"/> + <param name="bed" type="data" format="bed" label="Select a bed file describing the genomic regions to analyze" /> + <param name="method" type="boolean" falsevalue="bedtools" checked="false" truevalue="pysam" + help="coverage is computed using bedtools multicov (default) or pysam module" + label="Compute coverage with pysam (bedtools by default)" /> +</inputs> <outputs> - <data format="tabular" name="bedtools_table" label="bedtools multicov output" /> + <data format="tabular" name="coverage_dataframe" label="coverage table" /> <data format="pdf" name="distribution" label="Cumulative distribution of region coverages" /> </outputs> @@ -47,9 +60,17 @@ <test> <param name="inputs" value="sample1,sample2,sample3" ftype="bam"/> <param name="bed" value="probes.bed" ftype="bed"/> - <output file="coverage.tab" name="bedtools_table" /> + <param name="method" value="bedtools" /> + <output file="coverage.tab" name="coverage_dataframe" /> <output file="graph.pdf" name="distribution" /> </test> + <test> + <param name="inputs" value="sample1,sample2,sample3" ftype="bam"/> + <param name="bed" value="probes.bed" ftype="bed"/> + <param name="method" value="pysam" /> + <output file="coverage_pysam.tab" name="coverage_dataframe" /> + <output file="graph_pysam.pdf" name="distribution" /> + </test> </tests> |
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| diff -r ebe5ec2e244d -r 35d2db3753d9 test-data/coverage_pysam.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/coverage_pysam.tab Sun Sep 24 13:34:16 2017 -0400 |
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| b'@@ -0,0 +1,781 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