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182 lines
7.1 KiB
Python
Executable File
182 lines
7.1 KiB
Python
Executable File
#!/usr/bin/python
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import os.path
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import sys
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import optparse
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import bedClass
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from bedClass import *
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import vcfClass
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from vcfClass import *
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import tools
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from tools import *
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if __name__ == "__main__":
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main()
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# Intersect two vcf files. It is assumed that the two files are
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# sorted by genomic coordinates and the reference sequences are
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# in the same order.
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def intersectVcf(v1, v2, priority, outputFile):
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success1 = v1.getRecord()
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success2 = v2.getRecord()
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currentReferenceSequence = v1.referenceSequence
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# As soon as the end of either file is reached, there can be no
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# more intersecting SNPs, so terminate.
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while success1 and success2:
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if v1.referenceSequence == v2.referenceSequence and v1.referenceSequence == currentReferenceSequence:
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if v1.position == v2.position:
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writeVcfRecord(priority, v1, v2, outputFile)
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success1 = v1.getRecord()
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success2 = v2.getRecord()
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elif v2.position > v1.position: success1 = v1.parseVcf(v2.referenceSequence, v2.position, False, None)
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elif v1.position > v2.position: success2 = v2.parseVcf(v1.referenceSequence, v1.position, False, None)
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else:
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if v1.referenceSequence == currentReferenceSequence: success1 = v1.parseVcf(v2.referenceSequence, v2.position, False, None)
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elif v2.referenceSequence == currentReferenceSequence: success2 = v2.parseVcf(v1.referenceSequence, v1.position, False, None)
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# If the last record for a reference sequence is the same for both vcf
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# files, they will both have referenceSequences different from the
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# current reference sequence. Change the reference sequence to reflect
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# this and proceed.
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else:
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if v1.referenceSequence != v2.referenceSequence:
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print >> sys.stderr, "ERROR: Reference sequences for both files are unexpectedly different."
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print >> sys.stderr, "Check that both files contain records for the following reference sequences:"
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print >> sys.stderr, "\t", v1.referenceSequence, " and ", v2.referenceSequence
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exit(1)
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currentReferenceSequence = v1.referenceSequence
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# Intersect a vcf file and a bed file. It is assumed that the
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# two files are sorted by genomic coordinates and the reference
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# sequences are in the same order.
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def intersectVcfBed(v, b, outputFile):
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successb = b.getRecord()
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successv = v.getRecord()
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currentReferenceSequence = v.referenceSequence
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# As soon as the end of the first file is reached, there are no
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# more intersections and the program can terminate.
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while successv:
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if v.referenceSequence == b.referenceSequence:
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if v.position < b.start: successv = v.parseVcf(b.referenceSequence, b.start, False, None)
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elif v.position > b.end: successb = b.parseBed(v.referenceSequence, v.position)
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else:
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outputFile.write(v.record)
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successv = v.getRecord()
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else:
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if v.referenceSequence == currentReferenceSequence: successv = v.parseVcf(b.referenceSequence, b.start, False, None)
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if b.referenceSequence == currentReferenceSequence: successb = b.parseBed(v.referenceSequence, v.position)
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currentReferenceSequence = v.referenceSequence
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def main():
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# Parse the command line options
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usage = "Usage: vcfPytools.py intersect [options]"
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parser = optparse.OptionParser(usage = usage)
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parser.add_option("-i", "--in",
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action="append", type="string",
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dest="vcfFiles", help="input vcf files")
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parser.add_option("-b", "--bed",
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action="store", type="string",
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dest="bedFile", help="input bed vcf file")
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parser.add_option("-o", "--out",
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action="store", type="string",
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dest="output", help="output vcf file")
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parser.add_option("-f", "--priority-file",
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action="store", type="string",
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dest="priorityFile", help="output records from this vcf file")
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(options, args) = parser.parse_args()
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# Check that a single vcf file is given.
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if options.vcfFiles == None:
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parser.print_help()
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print >> sys.stderr, "\nAt least one vcf file (--in, -i) is required for performing intersection."
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exit(1)
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elif len(options.vcfFiles) > 2:
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parser.print_help()
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print >> sys.stderr, "\nAt most, two vcf files (--in, -i) can be submitted for performing intersection."
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exit(1)
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elif len(options.vcfFiles) == 1 and not options.bedFile:
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parser.print_help()
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print >> sys.stderr, "\nIf only one vcf file (--in, -i) is specified, a bed file is also required for performing intersection."
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exit(1)
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# Set the output file to stdout if no output file was specified.
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outputFile, writeOut = setOutput(options.output) # tools.py
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# If intersecting with a bed file, call the bed intersection routine.
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if options.bedFile:
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v = vcf() # Define vcf object.
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b = bed() # Define bed object.
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# Open the files.
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v.openVcf(options.vcfFiles[0])
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b.openBed(options.bedFile)
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# Read in the header information.
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v.parseHeader(options.vcfFiles[0], writeOut)
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taskDescriptor = "##vcfPytools=intersect " + options.vcfFiles[0] + ", " + options.bedFile
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writeHeader(outputFile, v, False, taskDescriptor) # tools.py
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# Intersect the vcf file with the bed file.
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intersectVcfBed(v, b, outputFile)
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# Check that the input files had the same list of reference sequences.
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# If not, it is possible that there were some problems.
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checkReferenceSequenceLists(v.referenceSequenceList, b.referenceSequenceList) # tools.py
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# Close the files.
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v.closeVcf(options.vcfFiles[0])
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b.closeBed(options.bedFile)
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else:
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priority = setVcfPriority(options.priorityFile, options.vcfFiles)
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v1 = vcf() # Define vcf object.
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v2 = vcf() # Define vcf object.
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# Open the vcf files.
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v1.openVcf(options.vcfFiles[0])
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v2.openVcf(options.vcfFiles[1])
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# Read in the header information.
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v1.parseHeader(options.vcfFiles[0], writeOut)
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v2.parseHeader(options.vcfFiles[1], writeOut)
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if priority == 3:
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v3 = vcf() # Generate a new vcf object that will contain the header information of the new file.
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mergeHeaders(v1, v2, v3) # tools.py
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v1.processInfo = True
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v2.processInfo = True
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else: checkDataSets(v1, v2)
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#print v1.samplesList
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#print v2.samplesList
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# Check that the header for the two files contain the same samples.
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if v1.samplesList != v2.samplesList:
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print >> sys.stderr, "vcf files contain different samples (or sample order)."
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exit(1)
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else:
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taskDescriptor = "##vcfPytools=intersect " + v1.filename + ", " + v2.filename
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if priority == 3: writeHeader(outputFile, v3, False, taskDescriptor)
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elif (priority == 2 and v2.hasHeader) or not v1.hasHeader: writeHeader(outputFile, v2, False, taskDescriptor) # tools.py
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else: writeHeader(outputFile, v1, False, taskDescriptor) # tools.py
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# Intersect the two vcf files.
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intersectVcf(v1, v2, priority, outputFile)
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# Check that the input files had the same list of reference sequences.
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# If not, it is possible that there were some problems.
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checkReferenceSequenceLists(v1.referenceSequenceList, v2.referenceSequenceList) # tools.py
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# Close the vcf files.
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v1.closeVcf(options.vcfFiles[0])
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v2.closeVcf(options.vcfFiles[1])
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# End the program.
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return 0
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