def trim4x(inFqFileName, outFqFilePrefix, trimLen):
if inFqFileName == 'stdin':
inFqFile = sys.stdin
else:
inFqFile = open(inFqFileName)
outFqFile1 = open('%s.1.fastq' % outFqFilePrefix, 'w')
outFqFile2 = open('%s.2.fastq' % outFqFilePrefix, 'w')
while 1:
line = inFqFile.readline()
if not line:
break
seq = inFqFile.readline()[:-1]
if line[0] != '@':
raise Exception
seqN = line[1:].rstrip().split(' ')[0]
inFqFile.readline()
qual = inFqFile.readline()[:-1]
if 'N' in seq[:trimLen] or 'N' in seq[-trimLen:]:
continue
outFqFile1.write('@%s/1\n%s\n+\n%s\n' %
(seqN, seq[:trimLen], qual[:trimLen]))
outFqFile2.write(
'@%s/2\n%s\n+\n%s\n' %
(seqN, mybasic.rc(seq[-trimLen:]), mybasic.rev(qual[-trimLen:])))
outFqFile1.close()
outFqFile2.close()
def trim4x(inFqFileName, outFqFilePrefix, trimLen):
if inFqFileName == "stdin":
inFqFile = sys.stdin
else:
inFqFile = open(inFqFileName)
outFqFile1 = open("%s.1.fastq" % outFqFilePrefix, "w")
outFqFile2 = open("%s.2.fastq" % outFqFilePrefix, "w")
while 1:
line = inFqFile.readline()
if not line:
break
seq = inFqFile.readline()[:-1]
if line[0] != "@":
raise Exception
seqN = line[1:].rstrip().split(" ")[0]
inFqFile.readline()
qual = inFqFile.readline()[:-1]
if "N" in seq[:trimLen] or "N" in seq[-trimLen:]:
continue
outFqFile1.write("@%s/1\n%s\n+\n%s\n" % (seqN, seq[:trimLen], qual[:trimLen]))
outFqFile2.write("@%s/2\n%s\n+\n%s\n" % (seqN, mybasic.rc(seq[-trimLen:]), mybasic.rev(qual[-trimLen:])))
outFqFile1.close()
outFqFile2.close()
def make_samse(ifileN, ofileN):
headerL = make_header('/data1/Sequence/ucsc_hg19/hg19.chrom.sizes')
# ofile = open(ofileN, 'w')
for header in headerL:
print header
# ofile.write('%s\n' % header)
result = mygsnap.gsnapFile('/pipeline/test_ini_gsnap2sam/S022_single.gsnap',False)
#result = mygsnap.gsnapFile('/pipeline/test_ini_gsnap2sam/test.gsnap',False)
#result = mygsnap.gsnapFile('/pipeline/test_ini_gsnap2sam/S022_pair.gsnap',True)
## for unpaired
for r in result:
qname = r.rid()
flag = 0x0
rname = '*'
pos = 0
mapq = 0
cigar = ''
rnext = '*' ## assume --npath=1 (maximum 1 alignment per read)
pnext = 0 ## assume --npath=1 (maximum 1 alignment per read)
tlen = 0 ## assume --npath=1 (maximum 1 alignment per read)
seq = r.seq()
qual = r.qual()
extra = 'NH:i:1\tHI:i:1' ## assume --npath=1 (maximum 1 alignment per read)
if r.nLoci > 1:
flag = flag | 0x4
cigar = '*'
new_cigar = '*'
extra = ''
print ('%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s' % (qname, flag, rname, pos, mapq, new_cigar, rnext, pnext, tlen, seq, qual, extra))
else:
if r.pairRel == '(transloc)':
match = r.matchL()[0]
segL = match.getSegInfo()
mapq = segL[0].mapq
seq = r.seq()
qual = r.qual()
for seg in segL:
flag = 0x0
(strand, rname, pos1, pos2) = re.search('([\+\-])(.*):([0-9]+)\.\.([0-9]+)', seg.seg[2]).groups()
pos = min(int(pos1), int(pos2))
(cigar,clip) = seg.toCIGAR_trans()
if clip < 0: ## first half
seq2 = seq[:clip]
qual2 = qual[:clip]
else: ## second half
seq2 = seq[clip:]
qual2 = qual[clip:]
if strand == '-':
flag = flag | 0x10
seq2 = mybasic.rc(seq2)
qual2 = mybasic.rev(qual2)
# print qname,seg.toCIGAR_trans()
print ('%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s' % (qname, flag, rname, pos, mapq, cigar, rnext, pnext, tlen, seq2, qual2, extra))
else:
match = r.matchL()[0] ## assume --npath=1 (maximum 1 alignment per read)
segL = match.getSegInfo()
(strand, rname, pos1, pos2) = re.search('([\+\-])(.*):([0-9]+)\.\.([0-9]+)', segL[0].seg[2]).groups()
pos = min(int(pos1), int(pos2))
mapq = segL[0].mapq
seg_nm = segL[0].numSub
cigar2 = match.toCIGAR()
# print qname, match.toCIGAR()
if segL[0].start != '' and segL[0].start != '0':
cigar = str(segL[0].start) + 'S'
if strand == '-':
cigar = str(segL[0].numMatch + segL[0].numSub) + 'M' + cigar
if segL[0].ins != '' and segL[0].ins != '0':
cigar = str(segL[0].ins) + 'I' + cigar
else:
cigar = cigar + str(segL[0].numMatch + segL[0].numSub) + 'M'
if segL[0].ins != '' and segL[0].ins != '0':
cigar = cigar + str(segL[0].ins) + 'I'
if len(segL) == 1:
new_cigar = segL[0].toCIGAR(True)
else:
new_cigar = segL[0].toCIGAR()
prev_cigar = new_cigar
index = 0
for seg in segL[1:]:
index = index + 1
if index == (len(segL) - 1):
final = True
else:
final = False
rm = re.search('([\+\-])(.*):([0-9]+)\.\.([0-9]+)', seg.seg[2]).groups()
match = str(seg.numMatch + seg.numSub) + 'M'
if seg.ins != '' and seg.ins != '0':
ins = str(seg.ins) + 'I'
else:
ins = ''
if pos == 0 or pos > min(int(rm[2]), int(rm[3])):
pos = min(int(rm[2]), int(rm[3]))
if strand == '-':
dist = int(pos2) - int(rm[2]) - 1
if dist > 0:
cigar = match + ins + str(dist) + 'N' + cigar
else:
cigar = match + ins + cigar
else:
dist = int(rm[2]) - int(pos2) - 1
if dist > 0:
cigar = cigar + str(dist) + 'N' + match + ins
else:
cigar = cigar + match + ins
seg_nm = seg_nm + seg.numSub
pos1 = rm[2]
pos2 = rm[3]
cur_cigar = seg.toCIGAR(final)
if strand == '-':
if dist > 0 and 'D' not in prev_cigar and 'I' not in prev_cigar:
new_cigar = cur_cigar + str(dist) + 'N' + new_cigar
else:
new_cigar = cur_cigar + new_cigar
else:
if dist > 0 and 'D' not in prev_cigar and 'I' not in prev_cigar:
new_cigar = new_cigar + str(dist) + 'N' + cur_cigar
else:
new_cigar = new_cigar + cur_cigar
prev_cigar = cur_cigar
if segL[-1].end != '' and segL[-1].end != '0': ## last segment
if strand == '-':
cigar = str(segL[-1].end) + 'S' + cigar
else:
cigar = cigar + str(segL[-1].end) + 'S'
extra = extra + ('\tNM:i:%s' % seg_nm)
if strand == '-':
flag = flag | 0x10
seq = mybasic.rc(seq)
qual = mybasic.rev(qual)
## print ('%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s' % (qname, flag, rname, pos, mapq, cigar, rnext, pnext, tlen, seq, qual, extra))
print ('%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s' % (qname, flag, rname, pos, mapq, cigar2, rnext, pnext, tlen, seq, qual, extra))
def make_samse(ifileN, ofileN):
headerL = make_header('/data1/Sequence/ucsc_hg19/hg19.chrom.sizes')
# ofile = open(ofileN, 'w')
for header in headerL:
print header
# ofile.write('%s\n' % header)
result = mygsnap.gsnapFile(
'/pipeline/test_ini_gsnap2sam/S022_single.gsnap', False)
#result = mygsnap.gsnapFile('/pipeline/test_ini_gsnap2sam/test.gsnap',False)
#result = mygsnap.gsnapFile('/pipeline/test_ini_gsnap2sam/S022_pair.gsnap',True)
## for unpaired
for r in result:
qname = r.rid()
flag = 0x0
rname = '*'
pos = 0
mapq = 0
cigar = ''
rnext = '*' ## assume --npath=1 (maximum 1 alignment per read)
pnext = 0 ## assume --npath=1 (maximum 1 alignment per read)
tlen = 0 ## assume --npath=1 (maximum 1 alignment per read)
seq = r.seq()
qual = r.qual()
extra = 'NH:i:1\tHI:i:1' ## assume --npath=1 (maximum 1 alignment per read)
if r.nLoci > 1:
flag = flag | 0x4
cigar = '*'
new_cigar = '*'
extra = ''
print('%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s' %
(qname, flag, rname, pos, mapq, new_cigar, rnext, pnext,
tlen, seq, qual, extra))
else:
if r.pairRel == '(transloc)':
match = r.matchL()[0]
segL = match.getSegInfo()
mapq = segL[0].mapq
seq = r.seq()
qual = r.qual()
for seg in segL:
flag = 0x0
(strand, rname, pos1,
pos2) = re.search('([\+\-])(.*):([0-9]+)\.\.([0-9]+)',
seg.seg[2]).groups()
pos = min(int(pos1), int(pos2))
(cigar, clip) = seg.toCIGAR_trans()
if clip < 0: ## first half
seq2 = seq[:clip]
qual2 = qual[:clip]
else: ## second half
seq2 = seq[clip:]
qual2 = qual[clip:]
if strand == '-':
flag = flag | 0x10
seq2 = mybasic.rc(seq2)
qual2 = mybasic.rev(qual2)
# print qname,seg.toCIGAR_trans()
print('%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s' %
(qname, flag, rname, pos, mapq, cigar, rnext, pnext,
tlen, seq2, qual2, extra))
else:
match = r.matchL()[
0] ## assume --npath=1 (maximum 1 alignment per read)
segL = match.getSegInfo()
(strand, rname, pos1,
pos2) = re.search('([\+\-])(.*):([0-9]+)\.\.([0-9]+)',
segL[0].seg[2]).groups()
pos = min(int(pos1), int(pos2))
mapq = segL[0].mapq
seg_nm = segL[0].numSub
cigar2 = match.toCIGAR()
# print qname, match.toCIGAR()
if segL[0].start != '' and segL[0].start != '0':
cigar = str(segL[0].start) + 'S'
if strand == '-':
cigar = str(segL[0].numMatch +
segL[0].numSub) + 'M' + cigar
if segL[0].ins != '' and segL[0].ins != '0':
cigar = str(segL[0].ins) + 'I' + cigar
else:
cigar = cigar + str(segL[0].numMatch +
segL[0].numSub) + 'M'
if segL[0].ins != '' and segL[0].ins != '0':
cigar = cigar + str(segL[0].ins) + 'I'
if len(segL) == 1:
new_cigar = segL[0].toCIGAR(True)
else:
new_cigar = segL[0].toCIGAR()
prev_cigar = new_cigar
index = 0
for seg in segL[1:]:
index = index + 1
if index == (len(segL) - 1):
final = True
else:
final = False
rm = re.search('([\+\-])(.*):([0-9]+)\.\.([0-9]+)',
seg.seg[2]).groups()
match = str(seg.numMatch + seg.numSub) + 'M'
if seg.ins != '' and seg.ins != '0':
ins = str(seg.ins) + 'I'
else:
ins = ''
if pos == 0 or pos > min(int(rm[2]), int(rm[3])):
pos = min(int(rm[2]), int(rm[3]))
if strand == '-':
dist = int(pos2) - int(rm[2]) - 1
if dist > 0:
cigar = match + ins + str(dist) + 'N' + cigar
else:
cigar = match + ins + cigar
else:
dist = int(rm[2]) - int(pos2) - 1
if dist > 0:
cigar = cigar + str(dist) + 'N' + match + ins
else:
cigar = cigar + match + ins
seg_nm = seg_nm + seg.numSub
pos1 = rm[2]
pos2 = rm[3]
cur_cigar = seg.toCIGAR(final)
if strand == '-':
if dist > 0 and 'D' not in prev_cigar and 'I' not in prev_cigar:
new_cigar = cur_cigar + str(dist) + 'N' + new_cigar
else:
new_cigar = cur_cigar + new_cigar
else:
if dist > 0 and 'D' not in prev_cigar and 'I' not in prev_cigar:
new_cigar = new_cigar + str(dist) + 'N' + cur_cigar
else:
new_cigar = new_cigar + cur_cigar
prev_cigar = cur_cigar
if segL[-1].end != '' and segL[-1].end != '0': ## last segment
if strand == '-':
cigar = str(segL[-1].end) + 'S' + cigar
else:
cigar = cigar + str(segL[-1].end) + 'S'
extra = extra + ('\tNM:i:%s' % seg_nm)
if strand == '-':
flag = flag | 0x10
seq = mybasic.rc(seq)
qual = mybasic.rev(qual)
## print ('%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s' % (qname, flag, rname, pos, mapq, cigar, rnext, pnext, tlen, seq, qual, extra))
print('%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s' %
(qname, flag, rname, pos, mapq, cigar2, rnext, pnext,
tlen, seq, qual, extra))
