def checkReferenceAllels(refFile, siteFile):
from XiaoweiLib import GenomeSequence
gs = GenomeSequence()
chroms = gs.open(refFile)
logger.info("Load reference file: " + refFile +
" (%d chromosomes)" % chroms)
msg = "Error: Found mismatched reference alleles at %s:%d. [%s in " + siteFile + " vs. %s in " + refFile + "]"
mismatchedRefAllele = 0
for ln in myopen(siteFile):
fd = ln.strip().split()
if fd[0].lower().startswith('chr'): continue
chrom, pos, rsid, ref, alt = fd[:5]
pos = int(pos)
trueRef = gs.getBase1(chrom, pos)
if trueRef.lower() != ref.lower():
mismatchedRefAllele += 1
logger.warn(msg % (chrom, pos, ref, trueRef))
if mismatchedRefAllele == 0:
logger.info("No mismatched reference alleles detected.")
else:
logger.info(
"Detected %d mismatched reference alleles. Please fix and rerun this script."
% mismatchedRefAllele)
sys.exit(1)
return 0
def getVariant(fn):
ret = -1
d = re.compile(r'Total \[ (\d+) \] variants are used to calculate autosomal kinship matrix.')
for ln in myopen(fn):
res = d.search(ln)
if res:
ret = res.groups()[0]
return int(ret)
def loadKinship(fn):
ids = []
kin = []
ncol = -1
for i, ln in enumerate(myopen(fn)):
fd = ln.strip().split()
if i == 0:
ncol = len(fd)
continue
ids.append(fd[:2])
kin.append([float(i) for i in fd[2:]])
nsample = ncol - 2
if len(ids) != nsample or \
any([nsample != len(i) for i in kin]):
print >> sys.stderr, "Dimension not match in ", fn
print >> sys.stderr, "Kinship file %s with %d samples loaded" % (fn, nsample)
return ids, kin
continue
assert (len(val) == 2), i
pileupId[i[0]] = val
## print pileupId
logger.info("%d sample id loaded" % len(pileupId))
# covFile = open(outPrefix + '.coverage', 'w')
# refCountFile = open(outPrefix + '.refCount', 'w')
# printHeader(colDict, mapRef, covFile)
# printHeader(colDict, mapRef, refCountFile)
#logFile = open(arg_outPrefix + '.log', 'w')
from collections import Counter
seqFile = open(arg_outPrefix + '.seq', 'w')
for fn in fns:
res = {}
for ln in myopen(fn): # loop each pileup file
fd = ln.strip().split()
if len(fd) == 4:
## after samtools 1.0.18, trancated pileup lines will be outputted
## and we will need to ignore them
chrom, pos, ref, depth = fd
refCount, altCount, qual = 0, 0, 0
elif len(fd) == 6:
chrom, pos, ref, depth, reads, quals = ln.strip().split()
try:
refCount, altCount = count(ref, reads)
qual = calculateMeanQuality(quals)
except:
logger.warn(
"Cannot parse pileup data, entering debug mode ...")