98 lines
2.9 KiB
Python
98 lines
2.9 KiB
Python
#!/usr/bin/env Python
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import sys
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debug = False
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print("Merging:")
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# open files for reading
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vcfInputFiles = []
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vcfOutputFile = ""
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for arg in sys.argv:
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if( arg.endswith("Fields.py") ):
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# do nothing
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continue
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else:
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if ( arg.startswith("I=") ):
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input1 = arg.strip().split("I=")[1]
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input2 = input1.split(",")
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for vcfInput in input2:
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print(vcfInput)
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vcfInputFiles.append(vcfInput)
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elif ( arg.startswith("O=") ):
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vcfOutputFile=open(arg.strip().split("O=")[1],'w')
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else:
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print("Unsupported argument: "+arg)
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sys.exit()
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lines = 0
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# the proper (albeit slower) way to do this is to read the info fields
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# into a dict and then iterate through the keys
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infodict = dict()
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for inFile in vcfInputFiles:
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# for each file
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for line in open(inFile).readlines():
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# for each line
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if ( line.startswith("#") ):
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# do nothing
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continue
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else:
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spline = line.strip().split()
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chrompos = spline[0]+":"+spline[1]
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info = spline[7]
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if ( chrompos in infodict ):
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if ( info == "." ):
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# do nothing
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continue
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else:
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curInfo = infodict[chrompos]
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if ( curInfo == "." or curInfo == ""):
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newInfo = info
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else:
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# now we need to parse the fields
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curinfofields = set(curInfo.split(";"))
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newinfofields = set(info.split(";"))
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curinfofields.update(newinfofields)
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newInfo = ";".join(curinfofields)
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infodict[chrompos] = newInfo
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#print(newInfo)
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else:
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infodict[chrompos] = info
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# dictionary has been constructed; now just iterate through the first vcf
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# and update the info field, printing to the output file
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if ( debug ):
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for key in infodict:
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print(infodict[key])
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for line in open(vcfInputFiles[0]).readlines():
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line = line.strip()
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if ( line.startswith("#") ):
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# this is a header
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vcfOutputFile.write(line+"\n")
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else:
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# this is a real line
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spline = line.split()
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outstring = ""
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fieldno = 0
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for field in spline:
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#print("fieldno="+str(fieldno))
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if ( fieldno == 7 ):
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outstring = outstring+infodict[spline[0]+":"+spline[1]]+"\t"
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fieldno = fieldno + 1
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else:
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outstring = outstring+field+"\t"
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fieldno = fieldno + 1
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# we wrote an extra \t, replace the last one with an \n
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outstring = outstring.strip()+"\n"
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vcfOutputFile.write(outstring)
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# and we're done
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