https://github.com/shorvath/MammalianMethylationConsortium
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
getCoverage.py
# Finds how many CG sites are targeted in each species for a selected set of Infinium 2 probes
import sys
import gzip
from collections import defaultdict
def main():
if len(sys.argv) != 3:
print ("Usage: python pickInf2Probes.py <probes file> <output file>")
exit(1)
probesFile = open(sys.argv[1], 'r')
oFile = open(sys.argv[2], 'w')
speciesCount = defaultdict(int)
for line in probesFile:
splitLine = line.strip().split("\t")
species = splitLine[24].split(",")
for curSpecies in species:
if (curSpecies == "A"):
print(line)
speciesCount[curSpecies] += 1
for species in sorted(speciesCount.keys()):
if (species != "hg19"):
oFile.write(species + " " + str(speciesCount[species]) + "\n")
oFile.close()
probesFile.close()
main()