def main():
"""The main function
"""
parser = cmdline_parser()
args = parser.parse_args()
if args.verbose:
LOG.setLevel(logging.INFO)
if args.debug:
LOG.setLevel(logging.DEBUG)
# file check
#
for (filename, descr, direction, mandatory) in [
(args.fbam_in, 'BAM input file', 'in', True),
(args.fbam_out, 'BAM output file', 'out', True),
(args.primer_pos_file, 'Primer positions file', 'in', True)]:
if not mandatory and not filename:
continue
if not filename:
parser.error("%s argument missing." % descr)
sys.exit(1)
if filename == '-':
continue
if direction == 'in' and not os.path.exists(filename):
LOG.fatal("file '{}' does not exist.\n".format(filename))
sys.exit(1)
if direction == 'out' and os.path.exists(filename) and not args.force_overwrite:
LOG.fatal("Refusing to overwrite existing file '{}'.\n".format(filename))
sys.exit(1)
if args.fbam_in == "-":
LOG.fatal("No streaming allow for input BAM (read twice)")
sys.exit(1)
# parse peaks and prep
#
peaks = pp.parse_primer_pos(open(args.primer_pos_file))
# summarize fw-start and rv-end positions in list. actually don't
# need anything else (i.e. the end positions)
peaks_fw_start_pos = [p.pos for p in peaks if p.ori == 'F']
peaks_rv_end_pos = [p.pos for p in peaks if p.ori == 'R']
dupreads_out = args.fbam_out.replace(".bam", ".dups.gz")
if os.path.exists(dupreads_out):
LOG.warn("Reusing {}".format(dupreads_out))
else:
with gzip.open(dupreads_out, 'w') as dupreads_fh:
find_primer_reads(args.fbam_in, peaks_fw_start_pos, peaks_rv_end_pos, dupreads_fh)
with pysam.Samfile(args.fbam_in, "rb") as sam_in:
with pysam.Samfile(args.fbam_out, "wb", template=sam_in) as sam_out:
with gzip.open(dupreads_out) as dupreads_fh:
mark_primer(sam_in, sam_out, dupreads_fh)
def main():
"""The main function
"""
parser = cmdline_parser()
(opts, args) = parser.parse_args()
if len(args):
parser.error("Unrecognized arguments found: %s." % (' '.join(args)))
sys.exit(1)
if opts.verbose:
LOG.setLevel(logging.INFO)
if opts.debug:
LOG.setLevel(logging.DEBUG)
# file check
#
for (filename, descr, direction, mandatory) in [
(opts.primer_pos_file, 'primer position input file', 'in', True),
(opts.bed_file, 'bed output file', 'out', False)
]:
if not mandatory and not filename:
continue
if not filename:
parser.error("%s argument missing." % descr)
sys.exit(1)
if filename == '-':
continue
if direction == 'in' and not os.path.exists(filename):
LOG.fatal("file '%s' does not exist.\n" % filename)
sys.exit(1)
if direction == 'out' and os.path.exists(
filename) and not opts.force_overwrite:
LOG.fatal("Refusing to overwrite existing file '%s'.\n" % filename)
sys.exit(1)
# primer length
#
if opts.primer_len < 0:
LOG.fatal("Negative primer length does not make sense")
sys.exit(1)
if not opts.seq_len or not opts.seq_name:
LOG.fatal(
"Missing sequence name or sequence length argument (or seq len 0)")
sys.exit(1)
seq_len = opts.seq_len
seq_name = opts.seq_name
if opts.bed_file == "-":
bed_fh = sys.stdout
else:
bed_fh = open(opts.bed_file, 'w')
primer_positions = pp.parse_primer_pos(open(opts.primer_pos_file))
primer_positions_to_incl_bed(primer_positions, bed_fh, opts.primer_len,
seq_len, seq_name)
if bed_fh != sys.stdout:
bed_fh.close()
def main():
"""
The main function
"""
parser = cmdline_parser()
args = parser.parse_args()
if args.verbose:
LOG.setLevel(logging.INFO)
if args.debug:
LOG.setLevel(logging.DEBUG)
# file check
#
for (filename, descr, direction, mandatory) in [
(args.fbam_in, 'BAM input file', 'in', True),
(args.fbam_out, 'BAM output file', 'out', True),
(args.primer_pos_file, 'Primer positions file', 'in', True)
]:
if not mandatory and not filename:
continue
if not filename:
parser.error("%s argument missing." % descr)
sys.exit(1)
if filename == '-':
continue
if direction == 'in' and not os.path.exists(filename):
LOG.fatal("file '{}' does not exist.\n".format(filename))
sys.exit(1)
if direction == 'out' and os.path.exists(
filename) and not args.force_overwrite:
LOG.fatal(
"Refusing to overwrite existing file '{}'.\n".format(filename))
sys.exit(1)
if args.fbam_in == "-":
LOG.fatal("No streaming allow for input BAM (read twice)")
sys.exit(1)
# parse peaks and prep
#
peaks = pp.parse_primer_pos(open(args.primer_pos_file))
# summarize fw-start and rv-end positions in list. actually don't
# need anything else (i.e. the end positions)
peaks_fw_start_pos = [p.pos for p in peaks if p.ori == 'F']
peaks_rv_end_pos = [p.pos for p in peaks if p.ori == 'R']
dupreads_out = args.fbam_out.replace(".bam", ".dups.gz")
if os.path.exists(dupreads_out):
LOG.warn("Reusing {}".format(dupreads_out))
else:
with gzip.open(dupreads_out, 'w') as dupreads_fh:
find_primer_reads(args.fbam_in, peaks_fw_start_pos,
peaks_rv_end_pos, dupreads_fh)
with pysam.Samfile(args.fbam_in, "rb") as sam_in:
with pysam.Samfile(args.fbam_out, "wb", template=sam_in) as sam_out:
with gzip.open(dupreads_out) as dupreads_fh:
mark_primer(sam_in, sam_out, dupreads_fh)
def main():
"""The main function
"""
parser = cmdline_parser()
(opts, args) = parser.parse_args()
if len(args):
parser.error("Unrecognized arguments found: %s." % (
' '.join(args)))
sys.exit(1)
if opts.verbose:
LOG.setLevel(logging.INFO)
if opts.debug:
LOG.setLevel(logging.DEBUG)
# file check
#
for (filename, descr, direction, mandatory) in [
(opts.fbam_in, 'BAM input file', 'in', True),
(opts.fbam_out, 'BAM output file', 'out', True),
(opts.primer_pos_file, 'Primer positions file', 'in', True),
]:
if not mandatory and not filename:
continue
if not filename:
parser.error("%s argument missing." % descr)
sys.exit(1)
if filename == '-':
continue
if direction == 'in' and not os.path.exists(filename):
LOG.fatal(
"file '%s' does not exist.\n" % filename)
sys.exit(1)
if direction == 'out' and os.path.exists(filename) and not opts.force_overwrite:
LOG.fatal(
"Refusing to overwrite existing file '%s'.\n" % filename)
sys.exit(1)
# region arguments
#
plpref = None
plpstart = None
plpend = None
if opts.plpstart or opts.plpend or opts.plpref:
if None in [opts.plpstart, opts.plpend, opts.plpref]:
LOG.fatal("If one of pileup-ref, -start or -end is given,"
" then all three must be given")
sys.exit(1)
if opts.plpstart < 1 or opts.plpstart >= opts.plpend:
LOG.fatal("Pileup start and end coordinates don't make sense")
sys.exit(1)
plpref = opts.plpref
plpstart = opts.plpstart-1
plpend = opts.plpend-1
# primer length
#
if opts.primer_len < 0:
LOG.fatal("Negative primer length does not make sense")
sys.exit(1)
primer_len = opts.primer_len
# parse peaks and prep
#
peaks = pp.parse_primer_pos(open(opts.primer_pos_file))
# summarize fw-start and rv-end positions in list. actually don't
# need anything else (i.e. the end positions)
peaks_fw_start_pos = [p.pos for p in peaks if p.ori == 'F']
peaks_rv_end_pos = [p.pos for p in peaks if p.ori == 'R']
sam_in = pysam.Samfile(opts.fbam_in, "rb")
sam_out = pysam.Samfile(opts.fbam_out, "wb", template=sam_in)
mark_primer(sam_in, sam_out,
peaks_fw_start_pos, peaks_rv_end_pos, primer_len,
(plpref, plpstart, plpend))
if sam_in != sys.stdin:
sam_in.close()
if sam_out != sys.stdout:
sam_out.close()
def main():
"""The main function
"""
parser = cmdline_parser()
(opts, args) = parser.parse_args()
if len(args):
parser.error("Unrecognized arguments found: %s." % (
' '.join(args)))
sys.exit(1)
if opts.verbose:
LOG.setLevel(logging.INFO)
if opts.debug:
LOG.setLevel(logging.DEBUG)
# file check
#
for (filename, descr, direction, mandatory) in [
(opts.bam_file, 'BAM input file', 'in', False),
(opts.primer_pos_file, 'primer position input file', 'in', True),
(opts.bed_file, 'bed output file', 'out', False),
]:
if not mandatory and not filename:
continue
if not filename:
parser.error("%s argument missing." % descr)
sys.exit(1)
if filename == '-':
continue
if direction == 'in' and not os.path.exists(filename):
LOG.fatal(
"file '%s' does not exist.\n" % filename)
sys.exit(1)
if direction == 'out' and os.path.exists(filename) and not opts.force_overwrite:
LOG.fatal(
"Refusing to overwrite existing file '%s'.\n" % filename)
sys.exit(1)
# primer length
#
if opts.primer_len < 0:
LOG.fatal("Negative primer length does not make sense")
sys.exit(1)
if not opts.bam_file:
if not opts.seq_len or not opts.seq_name:
LOG.fatal("Missing sequence name or sequence length argument")
sys.exit(1)
seq_len = opts.seq_len
seq_name = opts.seq_name
else:
if opts.seq_len or opts.seq_name:
LOG.fatal("BAM file given, so will derive seqlen and"
" seqname automatically, which were however"
" also given as arguments")
sys.exit(1)
sam_header = sam.sam_header(opts.bam_file)
sq_list = sam.sq_list_from_header(sam_header)
assert len(sq_list)==1, (
"Can only work with one sequence but found %d in %s" % (
(len(sq_list), opts.bam_file)))
seq_name = sq_list[0]
seq_len = sam.len_for_sq(sam_header, seq_name)
if opts.bed_file == "-":
bed_fh = sys.stdout
else:
bed_fh = open(opts.bed_file, 'w')
primer_positions = pp.parse_primer_pos(open(opts.primer_pos_file))
primer_positions_to_incl_bed(
primer_positions, bed_fh, opts.primer_len,
seq_len, seq_name)
if bed_fh != sys.stdout:
bed_fh.close()
def main():
"""The main function
"""
parser = cmdline_parser()
(opts, args) = parser.parse_args()
if len(args):
parser.error("Unrecognized arguments found: %s." % (
' '.join(args)))
sys.exit(1)
if opts.verbose:
LOG.setLevel(logging.INFO)
if opts.debug:
LOG.setLevel(logging.DEBUG)
# file check
#
for (filename, descr, direction, mandatory) in [
(opts.f_fa_in, 'Fasta input file', 'in', True),
(opts.f_fa_out, 'Fasta output file', 'out', True),
(opts.primers, 'Primer position file', 'in', True),
]:
if not mandatory and not filename:
continue
if not filename:
parser.error("%s argument missing." % descr)
sys.exit(1)
if filename == '-':
continue
if direction == 'in' and not os.path.exists(filename):
LOG.fatal(
"file '%s' does not exist.\n" % filename)
sys.exit(1)
if direction == 'out' and os.path.exists(filename) \
and not opts.force_overwrite:
LOG.fatal(
"Refusing to overwrite existing file '%s'.\n" % filename)
sys.exit(1)
# primer length
#
if opts.primer_len < 0:
LOG.fatal("Negative primer length does not make sense")
sys.exit(1)
primer_len = opts.primer_len
# parse primers and prep
#
primer_pos = pp.parse_primer_pos(open(opts.primers))
# summarize fw-start and rv-end positions in list. actually don't
# need anything else (i.e. the end positions)
primers_fw_start_pos = [p.pos for p in primer_pos if p.ori == 'F']
primers_rv_end_pos = [p.pos for p in primer_pos if p.ori == 'R']
if opts.f_fa_in == '-':
fh_fa_in = sys.stdin
else:
fh_fa_in = open(opts.f_fa_in, 'r')
if opts.f_fa_out == '-':
fh_fa_out = sys.stdout
else:
fh_fa_out = open(opts.f_fa_out, 'w')
mask_primer(fh_fa_in, fh_fa_out,
primers_fw_start_pos, primers_rv_end_pos, primer_len)
if fh_fa_in != sys.stdin:
fh_fa_in.close()
if fh_fa_out != sys.stdout:
fh_fa_out.close()
