import sys
import traceback
from mpileLineTemp import mpileLineTemp
from mpSample import mpSample
if __name__ == "__main__":
mpile_in = sys.argv[1]
with open(mpile_in) as pileFile:
for line in pileFile:
try:
pile_line = mpileLineTemp(line)
except Exception, e:
print sys.exc_info()[0]
print traceback.format_exc()
print line
pileFile.close()
"""
# any(lower <= postcode <= upper for (lower, upper) in [(1000, 2249), (2555, 2574), ...])
if any(
float(low) <= float(pos) <= float(high)
for (low, high) in TE_ranges[chrom]):
return False
return True
if __name__ == "__main__":
TE_file_loc, mp_file_loc = sys.argv[1], sys.argv[2]
loadTEranges(TE_file_loc)
trimmed_mp = open(
mp_file_loc[:mp_file_loc.find(".")] + "_TEremoved.mpileup", "w")
removed_sites = open(
mp_file_loc[:mp_file_loc.find(".")] + "_TE_sites.mpileup", "w")
with open(mp_file_loc) as mp_file:
for line in mp_file:
mp_line = mpileLineTemp(line)
if validRange(mp_line.chrom, mp_line.pos):
trimmed_mp.write(line)
else:
trimmed_mp.write(line)
removed_sites.close()
mp_file.close()
trimmed_mp.close()
return freqAltOther < freq
def minAltBases(mutant,minCount):
"""
Return if the given sample has >= minCount alt reads
"""
return (mutant.majorAltBaseCount >= minCount)
if __name__ == "__main__":
mpile_in = sys.argv[1]
with open(mpile_in) as mp_file:
for line in mp_file:
try:
mpLine = mpileLineTemp(line)
mutant = mpLine.getMutant()
# print mutant.__repr__()
if mutant != None:
if minAltBases(mutant,3):
# print "Pass min alt base"
if mutant.altReadBothStrands():
# print "pass alt both strands"
#print "Mutant: " + mutant.__repr__()
#print line
if maxFreqAltOtherSamples(mutant,mpLine.samples,0.02):
#print "pass max freq other samples"
print "pass"
except:
print sys.exc_info()[0]
