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