A helper script that will take a list of bams, a list of case sample IDs, and a list of control sample IDs, and generate a sample meta data yaml (which includes the bamfiles)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5482 348d0f76-0448-11de-a6fe-93d51630548a

python/createCaseControlMetaData.py

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