def _updateChimeraInfo(self,
suspicous_hits,
in_read_fn,
out_nc_fn,
out_c_fn,
primer_report_fn,
write_report_header=True):
"""
in_read_fn --- a fasta of full-length reads or a fasta of
non-full-length reads.
For each full-length read in in_read_fn FASTA file, detect whether
it is chimeric or not, and write its annotation to
primer_report_fn.
Return:
(num_nc, num_c, num_nc_bases, num_c_bases)
"""
logging.debug(
"Update chimera info for reads in {f} ".format(f=in_read_fn))
logging.debug(
"Write primer report to {rpt}".format(rpt=primer_report_fn))
num_nc, num_c, num_nc_bases, num_c_bases = 0, 0, 0, 0
with FastaReader(in_read_fn) as reader, \
FastaWriter(out_nc_fn) as writer, \
FastaWriter(out_c_fn) as writer_chimera, \
open(primer_report_fn, 'w') as reporter:
if write_report_header:
reporter.write(ReadAnnotation.header(delimiter=",") + "\n")
for r in reader:
# e.g. r.name="movie/zmw/0_100_CCS fiveend=1;threeend=100;"
readid = r.name.split()[0]
annotation = ReadAnnotation.fromString(
r.name, ignore_polyA=self.ignore_polyA)
if readid not in suspicous_hits: # Non-chimeric reads
# Primer of a primer-trimmed read can not be None.
# assert(annotation.primer is not None)
annotation.chimera = 0
num_nc += 1
num_nc_bases += len(r.sequence)
writer.writeRecord(annotation.toAnnotation(), r.sequence)
else: # chimeric reads
annotation.chimera = 1
num_c += 1
num_c_bases += len(r.sequence)
writer_chimera.writeRecord(annotation.toAnnotation(),
r.sequence)
reporter.write(annotation.toReportRecord(delimitor=",") + "\n")
return (num_nc, num_c, num_nc_bases, num_c_bases)
def _updateChimeraInfo(self, suspicous_hits, in_read_fn, out_nc_fn,
out_c_fn, primer_report_fn,
write_report_header=True):
"""
in_read_fn --- a fasta of full-length reads or a fasta of
non-full-length reads.
For each full-length read in in_read_fn FASTA file, detect whether
it is chimeric or not, and write its annotation to
primer_report_fn.
Return:
(num_nc, num_c, num_nc_bases, num_c_bases)
"""
logging.debug("Update chimera info for reads in {f} ".
format(f=in_read_fn))
logging.debug("Write primer report to {rpt}".
format(rpt=primer_report_fn))
num_nc, num_c, num_nc_bases, num_c_bases = 0, 0, 0, 0
with FastaReader(in_read_fn) as reader, \
FastaWriter(out_nc_fn) as writer, \
FastaWriter(out_c_fn) as writer_chimera, \
open(primer_report_fn, 'w') as reporter:
if write_report_header:
reporter.write(ReadAnnotation.header(delimiter=",") + "\n")
for r in reader:
# e.g. r.name="movie/zmw/0_100_CCS fiveend=1;threeend=100;"
readid = r.name.split()[0]
annotation = ReadAnnotation.fromString(r.name,
ignore_polyA=self.ignore_polyA)
if readid not in suspicous_hits: # Non-chimeric reads
# Primer of a primer-trimmed read can not be None.
# assert(annotation.primer is not None)
annotation.chimera = 0
num_nc += 1
num_nc_bases += len(r.sequence)
writer.writeRecord(annotation.toAnnotation(),
r.sequence)
else: # chimeric reads
annotation.chimera = 1
num_c += 1
num_c_bases += len(r.sequence)
writer_chimera.writeRecord(annotation.toAnnotation(),
r.sequence)
reporter.write(annotation.toReportRecord(delimitor=",") + "\n")
return (num_nc, num_c, num_nc_bases, num_c_bases)
