def load_file_to_dict(file_loc, sites):
"""
Dictionary format:
sites: {CHROM: {pos:(CC_info, GP_info), pos: (...)}, CHROM:{...}}
"""
with open(file_loc) as f:
for line in f:
mpile_site = mpileLine(line)
sites[mpile_site.chrom] = sites.get(mpile_site.chrom, {})
sites[mpile_site.chrom][mpile_site.pos] = \
sites[mpile_site.chrom].get(mpile_site.pos, [])
sites[mpile_site.chrom][mpile_site.pos].append(site_info(mpile_site))
return
return freq
if __name__ == "__main__":
mpile_in,mpile_out = sys.argv[1],sys.argv[2]
outFile = open(mpile_out,"w")
# min_alt = int(sys.argv[3])
min_freq = 0.3
with open(mpile_in) as mp_file:
for line in mp_file:
try:
mpLine = mpileLine(line)
if mpLine.chrom not in "pseudo0mitochondrionchloroplast":
mutant = mpLine.getMutant()
if mutant != None:
alt_freq = freq_all_samples(mutant.majorAltBase, mpLine.samples)
if alt_freq >= min_freq:
outFile.write(line)
else:
print alt_freq
except:
print "ERROR"
print sys.exc_info()[0]
GP_smpls = old_GP_smpls
#Assign idList to one of CC or GP smples
if "CC" in mpile_in:
idList = CC_smpls
elif "GP" in mpile_in:
idList = GP_smpls
else:
print "Error incorrect mpile_in name"
sys.exit()
##Loop though mpile file
with open(mpile_in) as mp_file:
for line in mp_file:
try:
mpLine = mpileLine(line)
mutant = mpLine.getMutant()
mutantID = mpLine.getMutantID(idList)
counts[mutantID] = counts.get(mutantID,0) + 1
except:
print sys.exc_info()[0]
print traceback.format_exc()
print line
#Write out counts dict to outFile
for key in counts.keys():
outFile.write(str(key) + ":" + str(counts[key]) + "\n")
from vcfDict import vcfDict
from vcfLine import vcfLine
from vcfSample import vcfSample
from mpileLine import mpileLine
if __name__ == "__main__":
mpile_in,vcf_in,csv_out = sys.argv[1],sys.argv[2],sys.argv[3]
#Load dictionary of sites in vcf_in file
vcfSites = vcfDict(vcf_in)
vcfSites.loadDict()
#Create output file for csv_out
outFile = open(csv_out,"w")
with open(mpile_in) as pileFile:
for line in pileFile:
try:
pile_line = mpileLine(line)
print pile_line.repr()
if vcfSites.siteExists(pile_line.siteID):
vcf_line = vcfLine(vcfSites.getLine(pile_line.siteID))
except Exception, e:
print sys.exc_info()[0]
print traceback.format_exc()
print line
outFile.close()
pileFile.close()
