62 lines
2.3 KiB
Python
62 lines
2.3 KiB
Python
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import sys
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import os
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import subprocess
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import shlex
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from optparse import OptionParser
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def parseInput(fList,ignoreExt = None):
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inNames = []
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for ele in fList:
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if ( ignoreExt != None and ele.endswith(ignoreExt) ):
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inFileNames.append(ele)
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if ( os.path.exists(ele) ):
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for line in open(ele).readlines():
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inNames.append(line.strip())
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return inNames
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def bamsWithSamples(bamList):
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cmdbase = "samtools view -H %s | grep SM | tr '\\t' '\\n' | grep SM | sed 's/SM://g' | uniq"
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sam2bam = dict()
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for bf in bamList:
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if ( not os.path.exists(bf) ):
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raise IOError("Bam file "+bf+" does not exist")
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cmd = cmdbase % bf
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proc = subprocess.Popen(cmd,shell=True,stdout=subprocess.PIPE)
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proc.wait()
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stdout = proc.stdout.readlines()
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if ( len(stdout) > 1 ):
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raise RuntimeError("The bam file "+bf+" contains multiple different sample entries")
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sm = stdout[0].strip()
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sam2bam[sm]=bf
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return sam2bam
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def runMain(opt,arg):
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bamFiles = bamsWithSamples(parseInput(opt.bam_files,"bam"))
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caseNames = set(parseInput(opt.cases))
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controlNames = set(parseInput(opt.controls))
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output = open(opt.output,'w')
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output.write("samples:")
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sample_base = "- id: %s\n properties:\n cohort: %s\n bam: %s"
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for s in bamFiles.keys():
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cc = "Unknown"
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if ( s in caseNames ):
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cc = "case"
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if ( s in controlNames ):
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cc = "control"
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output.write("\n" + sample_base % (s,cc,bamFiles[s]))
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output.close()
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def main():
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usage = "usage: %prog [options] arg"
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parser = OptionParser(usage)
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parser.add_option("-I","--bams",dest="bam_files",help="the bam files, as multiple arguments or a simple newline-delimited file",action="append")
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parser.add_option("-A","--case",dest="cases",action="append",help="A list of the case samples, as multiple arguments or a simple newline-delimited file")
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parser.add_option("-O","--control",dest="controls",action="append",help="A list of the control samples, multiple arguments or a newline-delimited file")
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parser.add_option("-o","--out",dest="output",action="store",help="Name of the output metadata file to write to")
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(options,args) = parser.parse_args()
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runMain(options,args)
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if __name__ == "__main__":
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main()
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