51 lines
1.5 KiB
Python
51 lines
1.5 KiB
Python
#!/bin/tcsh
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import os.path
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import sys
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from optparse import OptionParser
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from itertools import *
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def main():
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global OPTIONS
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usage = "usage: %prog [options] mode hg19Tohg18.chain"
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parser = OptionParser(usage=usage)
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# parser.add_option("-D", "--delete_while_archiving", dest="reallyDeleteInArchiveMode",
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# action='store_true', default=False,
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# help="if provided, we'll actually delete records when running in archive mode")
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(OPTIONS, args) = parser.parse_args()
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if len(args) != 1:
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parser.error("Requires exact 1 chain to analyze")
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hg192hg18 = args[0]
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writeChain(hg192hg18, "b37tohg18.chain", lambda x: hg2b(x, 2))
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writeChain(hg192hg18, "b37tob36.chain", lambda x: hg2b(hg2b(x, 2), 7))
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HG2BCONTIG = dict()
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for c in range(1, 23) + ["X", "Y"]:
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HG2BCONTIG["chr" + str(c)] = str(c)
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HG2BCONTIG["chrM"] = "MT"
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def hg2b(line, pos):
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parts = line.split()
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if len(parts) > pos and "chr" in parts[pos]:
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if parts[pos] in HG2BCONTIG:
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parts[pos] = HG2BCONTIG[parts[pos]]
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else:
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print 'Skipping ', parts[pos]
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return "\t".join(parts)
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def writeChain(inFile, outFile, transform):
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out = open(outFile, "w")
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for line in open(inFile):
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newLine = transform(line)
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#print 'newline', newLine
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if newLine != None:
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out.write(newLine)
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out.write("\n")
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out.close()
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if __name__ == "__main__":
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main()
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