https://github.com/shorvath/MammalianMethylationConsortium
Revision 3da9cc968671049f7a73e3dcd23821ad832f5617 authored by Adriana on 18 January 2021, 23:51:08 UTC, committed by Adriana on 18 January 2021, 23:51:08 UTC
1 parent 30d4605
Tip revision: 3da9cc968671049f7a73e3dcd23821ad832f5617 authored by Adriana on 18 January 2021, 23:51:08 UTC
Added CMAPS source code
Added CMAPS source code
Tip revision: 3da9cc9
pickProbes.py
# Selects probes based on a minimum number of species they have to cover
import sys
import gzip
from collections import defaultdict
def main():
if len(sys.argv) != 6:
print "Usage: python pickProbes.py <probes file> <infinium type> <number of species threshold> <output file> <probes/sites>"
exit(0)
probesFile = gzip.open(sys.argv[1], 'r')
infiniumType = int(sys.argv[2])
speciesThresh = int(sys.argv[3])
oFile = gzip.open(sys.argv[4], 'w')
probesOrSites = sys.argv[5]
alreadyPicked = defaultdict(bool)
for line in probesFile:
splitLine = line.strip().split('\t')
if infiniumType == 1:
if len(splitLine) < 10:
continue
species = splitLine[9].split(",")
else:
if len(splitLine) < 13:
continue
species = splitLine[12].split(",")
if len(species) >= speciesThresh:
if probesOrSites == "probes":
oFile.write(line)
else:
coord = int(splitLine[3])
if not alreadyPicked[(splitLine[2], coord)]:
oFile.write("chr" + splitLine[2] + "\t" + str(coord) + "\t" + str(coord + 2) + "\n")
alreadyPicked[(splitLine[2], coord)] = True
probesFile.close()
oFile.close()
main()
Computing file changes ...