def checkRef(name):
reffile = name +'RefT'
altfile = name + 'AltT'
hg19 = worldbase.Bio.Seq.Genome.HUMAN.hg19(download = True)
print "Loaded hg19"
ref = glob.json(reffile)
print "Loaded Ref"
alt = glob.json(altfile)
print "Loaded Alt"
flip = []
errors = []
keys = ref.keys()
for snppos in keys:
print snppos + '\t' + name
t = snppos.split('pos')
hg19snp = str(hg19[t[0]][int(t[1])-1]).upper()
refsnp = ref[snppos].upper()
altsnp = alt[snppos].upper()
if hg19snp == refsnp:
continue
elif hg19snp == altsnp:
flip.append(snppos)
else:
print "Error: Neither Ref nor Alt of SNP corresponds to hg19 sequence"
errors.append(snppos)
glob.dump(flip, name+'flips')
glob.dump(errors, name+'errors')
return [flip, errors]
def main(argv):
opts, args = getopt.getopt(argv,"a:ghc:i",["report=", "genonames="])
for opt, arg in opts:
if opt == '-a':
report = arg
print "processing array, getting snps {0}".format(report)
getarraysnps(arg)
[f, e] = parsegenotypes.checkRef(report)
parsegenotypes.flipArray(report, f)
parsegenotypes.filterzeros(report)
parsegenotypes.printtabarray(report)
elif opt == '-g':
processgenotypes()
elif opt == '-h':
processhapmap()
elif opt == '-c':
snps = glob.json('Array251Msnps')
if arg == '':
genofiles = names1KG
else:
genofiles = arg
combinegenos(genofiles, snps)
elif opt == "-i":
genofiles = names.append('hapmap')
def getpoollines(genofile, pool, out = "poolgenotype"):
output = open(out, 'w')
pool = glob.json(pool)
g = open(genofile)
lines = g.readlines()
g.close()
linenames = lines[0]
ln = linenames.split('\t')[1].split(',')
ln = map(lambda x: x.strip('\n'), ln)
print pool
poolinds = map(lambda x: ln.index(x), pool)
nl = [ln[i] for i in poolinds]
newlinenames = ','
newlinenames = reduce(lambda x,y: x + ',' + y, nl)
output.write(newlinenames + '\n')
for l in lines[1:]:
t = l.split('\t')
gs = t[1].split(',')
gs = map(lambda x: x.strip('\n'), gs)
if len(filter(lambda x: int(x)!=0, gs)) >0:
newl = t[0] + ','
newg = []
for i in range(0, len(gs)):
if i in poolinds:
newg.append(gs[i])
newg = reduce(lambda x,y: x + ',' + y, newg)
newl = newl + newg + '\n'
output.write(newl)
def printtabarray(arrayname): """output will be analyzed by R to find cell line frequencies """ output = open(arrayname+'Rinput', 'w') freq = glob.json(arrayname+'freq') for snp in freq.keys(): output.write(snp + '\t') output.write(str(freq[snp]) + '\n')
def filterzeros(arrayname): """take out those that are 0 """ freq = glob.json(arrayname+'freq') for snp in freq.keys(): if freq[snp] == 0 or math.isnan(freq[snp]): del freq[snp] glob.dump(freq, arrayname+'freq')
def parsehapmapchrom(chrom):
""" inputs: rsid hash (hash of snp positions and rsIDs)
hapmapchrN downloaded from hapmap3 site
people: list of cell line IDs that we are looking for
"""
hapmapfile = '../genotypes/hapmapchr'+str(chrom)
if 'rsid2poshash' not in os.listdir('./'):
makerhash()
else:
rshash = glob.json('rsid2poshash')
people = ['NA19140','NA19154','NA19173','NA19203','NA19206','NA19211','NA19222']
with open(hapmapfile) as f:
lines = f.readlines()
header = lines[0].split(' ')
rsidi = header.index('rs#')
snpi = header.index('alleles')
peoplewithgenos = filter(lambda x: x in header, people)
print peoplewithgenos
peoplei = map(lambda x: header.index(x), peoplewithgenos)
refhash = {}
althash = {}
out = open(hapmapfile+'genotype','w')
for l in lines[1:]:
t = l.split(' ')
rsid = t[rsidi]
snps = t[snpi].split('/')
ref = snps[0].upper()
alt = snps[1].upper()
genotypes = map(lambda x: t[x], peoplei)
genocount = map(lambda x: len(filter(lambda y: alt == y, x.upper())), genotypes)
try:
snppos = rshash[rsid]
newline = snppos + '\t'
newline = reduce(lambda x,y: x+str(y) + ',', [newline] + genocount)
out.write(newline+'\n')
refhash[snppos] = ref
althash[snppos] = alt
except KeyError:
pass
out.close()
return [refhash, althash]
def flipArray(arrayname, flip, error): """flip array snp frequencies (hash) 1-freq for those in snp list inputed as flip input is constructed in the original getarraysnps() function """ try: arrayfreq = glob.json(arrayname+'freq') except: "No array snp frequency file" for snp in flip: arrayfreq[snp] = 1 - arrayfreq[snp] for snp in error: del arrayfreq[snp] glob.dump(arrayfreq, arrayname+'freq')
def filterSNPs(name):
reffile = name +'Ref'
altfile = name + 'Alt'
[ref, alt] = map(lambda x: glob.json(x, ''), [reffile, altfile])
print "Loaded Ref {0}, Alt {1}".format(len(ref),len(alt))
keys = ref.keys()
complsnps = []
for snppos in keys:
if glob.compl[ref[snppos].upper()] == alt[snppos].upper() or ref[snppos].upper() == alt[snppos].upper():
complsnps.append(snppos)
del ref[snppos]
del alt[snppos]
print len(ref)
print len(alt)
glob.dump(ref, reffile+'T')
glob.dump(alt, altfile+'T')
return complsnps
if args.a:
print "processing array, getting snps {0}".format(args.a)
report = args.a
getarraysnps(report)
[f, e] = parsegenotypes.checkRef(report)
parsegenotypes.flipArray(report, f, e)
parsegenotypes.filterzeros(report)
parsegenotypes.printtabarray(report)
if args.g:
processgenotypes()
if args.hapmap:
processhapmap()
if args.init1KG:
#snps = glob.json('25M1.1snps')
snps = glob.json('MKReportbySNP1.txtsnps')
#combinegenos(names1KG, snps, 'Genos1kgArray25M')
combinegenos(names1KG, snps, 'Genos1kgArrayOmni')
if args.inithapmap:
snps = glob.json('Array25M1snps')
combinegenos('hapmap', snps, 'hapmapGenosArray25M', 1)
if args.pool:
#getpoollines('intercomb','pool1', 'pool1genotype')
# new arrays
#getpoollines('Genos1kgArray25M', 'pool1', 'pool1genotype')
#old arrays
getpoollines('Genos1kgArrayOmni', 'pool1', 'pool1genotypeOmni')