def filter(self, bam):
for read in self.parent.filter(bam):
if not read.is_unmapped:
read.tags = read.tags + [(self.tag, cigar_tostr(read.cigar))]
else:
read.tags = read.tags + [(self.tag, "*")]
yield read
def filter(self, bam):
for read in self.parent.filter(bam):
if not read.is_unmapped:
read.tags = read.tags + [(self.tag, cigar_tostr(read.cigar))]
else:
read.tags = read.tags + [(self.tag, '*')]
yield read
def export_read(bamfile, read, fields, out=sys.stdout):
cols = []
for field in fields:
if field == '-name':
cols.append(read.qname)
elif field == '-ref':
if read.tid == -1:
cols.append('*')
elif bamfile:
cols.append(bamfile.getrname(read.tid))
else:
cols.append('?')
elif field == '-pos':
cols.append(read.pos + 1) # output 1-based
elif field == '-strand':
cols.append('-' if read.is_reverse else '+')
elif field == '-cigar':
if read.cigar:
cols.append(cigar_tostr(read.cigar))
else:
cols.append('*')
elif field == '-flags':
cols.append(read.flag)
elif field == '-seq':
cols.append(read.seq)
elif field == '-qual':
cols.append(read.qual)
elif field == '-mapq':
cols.append(read.mapq)
elif field == '-nextref':
if read.rnext == -1:
cols.append('*')
elif bamfile:
cols.append(bamfile.getrname(read.rnext))
else:
cols.append('?')
elif field == '-nextpos':
if read.rnext == -1:
cols.append(0)
else:
cols.append(read.pnext + 1) # output 1-based
elif field == '-tlen':
cols.append(read.tlen)
elif field == '-isize':
cols.append(read.isize)
elif field[:5] == '-tag:':
if field[5:] == '*':
for tag, val in read.tags:
if type(val) == int:
cols.append('%s:i:%s' % (tag, val))
elif type(val) == float:
cols.append('%s:f:%s' % (tag, val))
elif len(val) == 1:
cols.append('%s:A:%s' % (tag, val))
else:
cols.append('%s:Z:%s' % (tag, val))
else:
try:
cols.append(read.opt(field[5:]))
except KeyError:
cols.append('')
out.write('%s\n' % '\t'.join([str(x) for x in cols]))
def export_read(bamfile, read, fields, out=sys.stdout):
cols = []
for field in fields:
if field == '-name':
cols.append(read.qname)
elif field == '-ref':
if read.tid == -1:
cols.append('*')
elif bamfile:
cols.append(bamfile.getrname(read.tid))
else:
cols.append('?')
elif field == '-pos':
cols.append(read.pos + 1) # output 1-based
elif field == '-strand':
cols.append('-' if read.is_reverse else '+')
elif field == '-cigar':
if read.cigar:
cols.append(cigar_tostr(read.cigar))
else:
cols.append('*')
elif field == '-flags':
cols.append(read.flag)
elif field == '-seq':
cols.append(read.seq)
elif field == '-qual':
cols.append(read.qual)
elif field == '-mapq':
cols.append(read.mapq)
elif field == '-nextref':
if read.rnext == -1:
cols.append('*')
elif bamfile:
cols.append(bamfile.getrname(read.rnext))
else:
cols.append('?')
elif field == '-nextpos':
if read.rnext == -1:
cols.append(0)
else:
cols.append(read.pnext + 1) # output 1-based
elif field == '-tlen':
cols.append(read.tlen)
elif field == '-isize':
cols.append(read.isize)
elif field[:5] == '-tag:':
if field[5:] == '*':
for tag, val in read.tags:
if type(val) == int:
cols.append('%s:i:%s' % (tag, val))
elif type(val) == float:
cols.append('%s:f:%s' % (tag, val))
elif len(val) == 1:
cols.append('%s:A:%s' % (tag, val))
else:
cols.append('%s:Z:%s' % (tag, val))
else:
try:
cols.append(read.opt(field[5:]))
except KeyError:
cols.append('')
out.write('%s\n' % '\t'.join([str(x) for x in cols]))
