def main(args):
option = "r" if args.samformat else "rb"
samfile = Samfile(args.bamfile, "rb")
ref_ids = [samfile.gettid(r) for r in samfile.references]
#Iterates over each read instead of each contig
reads_to_print = []
for aln in samfile.fetch(until_eof = True):
if pair_is_aligned(aln, ref_ids):
if args.read_pair == 1 and aln.is_read1:
reads_to_print.append(aln)
elif args.read_pair == 2 and aln.is_read2:
reads_to_print.append(aln)
elif args.read_pair == 0:
reads_to_print.append(aln)
if len(reads_to_print) >= 10000:
# Flush the reads collected
print_reads(reads_to_print)
reads_to_print = []
print_reads(reads_to_print)
def main(args):
option = "r" if args.samformat else "rb"
samfile = Samfile(args.bamfile, option)
ref_ids = [samfile.gettid(r) for r in samfile.references]
#Iterates over each read instead of each contig
reads_to_print_1 = []
reads_to_print_2 = []
reads_to_print_u = []
for aln in samfile.fetch(until_eof = True):
if aln.tid in ref_ids: # This read is aligned
if aln.rnext in ref_ids: # The mate is also aligned
if aln.is_read1:
reads_to_print_1.append(aln)
reads_to_print_1 = flush_reads(reads_to_print_1, args.R1)
elif aln.is_read2:
reads_to_print_2.append(aln)
reads_to_print_2 = flush_reads(reads_to_print_2, args.R2)
else:
reads_to_print_u.append(aln)
reads_to_print_u = flush_reads(reads_to_print_u, args.u)
print_reads(reads_to_print_1, args.R1)
print_reads(reads_to_print_2, args.R2)
print_reads(reads_to_print_u, args.u)
def bam_surject_msa(args):
"""
Caveats:
- flags are remained as original statuses
- remaining original values for MD, NM, and AS tags
- mate are given as unmapped
- same records are emited
"""
skip_flag = args.skip_flag
sam = Samfile(args.bam)
fasta = Fasta(open(args.msa_fasta))
mapped_ref_set = set(sam.references)
# setup output
if args.refnames is None:
refnames = [
'consensus{0}'.format(i) for i in xrange(len(args.msa_fastas))
]
else:
refnames = args.refnames
assert len(refnames) == len(
args.msa_fastas
), 'The number of refnames should be the same as that of msa_fastas.'
logging.info('Loading MSA fastas')
logging.info('Skip flag: %s', args.skip_flag)
fastas = []
ref_lens = []
target_ref_set = set()
for fn in args.msa_fastas:
with open(fn) as fp:
fasta = Fasta(fp)
fastas.append(fasta)
if len(fasta.contigs) == 0:
logging.error('Fasta file %s has no contigs', fn)
raise Exception('No contigs')
ref_lens.append(len(fasta.contigs[0]))
target_ref_set.update(fasta.names)
rest_refs = [r for r in sam.references if r not in target_ref_set]
logging.info('%s are included in surjection targets.', len(target_ref_set))
logging.info('%s are not included in surjection targets.', len(rest_refs))
if args.keep_rest:
logging.info('Rest of reference will be kept in surjected BAM file')
org_ref_len_map = dict(zip(sam.references, sam.lengths))
refnames.extend([r for r in rest_refs])
ref_lens.extend([org_ref_len_map[r] for r in rest_refs])
fastas.extend([None for r in rest_refs])
logging.info('Setting up output BAMs')
if args.output.endswith('.bam'):
mode = 'wb'
else:
mode = 'wh'
out = pysam.Samfile(args.output,
mode=mode,
reference_names=[refname],
reference_lengths=[ref_length])
# iteration
for refname, fasta in zip(refnames, fastas):
out_tid = out.gettid(refname)
if fasta is None:
logging.info('Transfering %s', refname)
src_tid = sam.gettid(refname)
for rec in sam.fetch(reference=refname):
if rec.flag & skip_flag:
continue
a = rec.__copy__()
a.reference_id = out_tid
if a.next_reference_id != src_tid: # pair on the same refs
a.next_reference_id = out_tid
else:
a.next_reference_id = -1 # unpair
a.next_reference_start = -1
out.write(a)
continue
logging.info('Surjecing to %s', refname)
query_refs = fasta.names
cc = _CigarChecker() if args.check else None
for qref in query_refs:
if qref not in mapped_ref_set:
logging.warning('%s is not found in original BAM file', qref)
continue
#a = pysam.AlignedSegment()
a = rec.__copy__()
#print (rec)
if not rec.is_unmapped:
org_cigar = Cigar(rec.cigartuples)
pos, cigar = mc.convert(rec.pos, org_cigar)
if org_cigar.query_length != cigar.query_length:
logging.error('Invalid cigar conversion for %s', rec.qname)
logging.error('org %s %s %s', rec.pos, org_cigar,
org_cigar.query_length)
logging.error('new %s %s %s', pos, cigar,
cigar.query_length)
s1 = pos
e1 = mc.get_pos(rec.pos + cigar.ref_length)
logging.error('ref %s-%s %s', s1, e1,
mc.get_ref_cigar(s1, e1))
logging.error('read %s', rec.seq)
logging.error('qref %s', q_aln.seq[s1:e1])
raise Exception('Incompatible Cigar')
cc and cc.check(rec, pos, cigar, org_cigar, mc, q_aln)
a.cigar = cigar.values
a.reference_start = pos
a.reference_id = out_tid
a.next_reference_id = -1 # this is required
a.next_reference_start = -1 # this is required
#a.flag = rec.flag
#orec.seq = '*'
#print (orec)
out.write(a)
