def _extend_contigs_with_bam(self, bam_in, out_prefix=None, output_all_useful_reads=False):
if out_prefix is not None:
fa_out1 = pyfastaq.utils.open_file_write(out_prefix + '_1.fa')
fa_out2 = pyfastaq.utils.open_file_write(out_prefix + '_2.fa')
keep_read_types = set([mapping.CAN_EXTEND_LEFT, mapping.CAN_EXTEND_RIGHT, mapping.KEEP])
if output_all_useful_reads:
keep_read_types.add(mapping.BOTH_UNMAPPED)
previous_sam = None
left_seqs = []
right_seqs = []
sam_reader = pysam.Samfile(bam_in, "rb")
for current_sam in sam_reader.fetch(until_eof=True):
if previous_sam is None:
previous_sam = current_sam
continue
previous_type, current_type = mapping.get_pair_type(previous_sam, current_sam, self._get_ref_length_sam_pair(sam_reader, previous_sam, current_sam), self.max_insert, min_clip=self.min_clip)
for sam, sam_type in [(previous_sam, previous_type), (current_sam, current_type)]:
if sam_type == mapping.CAN_EXTEND_LEFT:
name = mapping.get_ref_name(sam, sam_reader)
clipped = mapping.soft_clipped(sam)[0]
self.contigs[name].add_left_kmer(common.decode(sam.seq[:clipped]))
elif sam_type == mapping.CAN_EXTEND_RIGHT:
name = mapping.get_ref_name(sam, sam_reader)
self.contigs[name].add_right_kmer(common.decode(sam.seq[sam.qend:]))
if out_prefix is not None and sam_type in keep_read_types:
if sam.is_read1:
print(mapping.sam_to_fasta(sam), file=fa_out1)
else:
print(mapping.sam_to_fasta(sam), file=fa_out2)
previous_sam = None
if out_prefix is not None:
pyfastaq.utils.close(fa_out1)
pyfastaq.utils.close(fa_out2)
total_bases_added = 0
for ctg in self.contigs:
left_length, right_length = self.contigs[ctg].extend(self.ext_min_cov, self.ext_min_ratio, self.ext_bases)
if self.verbose:
print(' extend contig ' + ctg, 'new_length:' + str(len(self.contigs[ctg])), 'added_left:' + str(left_length), 'added_right:' + str(right_length), sep='\t')
self.contig_lengths[ctg].append([len(self.contigs[ctg]), left_length, right_length])
total_bases_added += left_length + right_length
return total_bases_added
def _extend_contigs_with_bam(self, bam_in, out_prefix=None, output_all_useful_reads=False):
if out_prefix is not None:
fa_out1 = pyfastaq.utils.open_file_write(out_prefix + '_1.fa')
fa_out2 = pyfastaq.utils.open_file_write(out_prefix + '_2.fa')
keep_read_types = set([mapping.CAN_EXTEND_LEFT, mapping.CAN_EXTEND_RIGHT, mapping.KEEP])
if output_all_useful_reads:
keep_read_types.add(mapping.BOTH_UNMAPPED)
previous_sam = None
left_seqs = []
right_seqs = []
sam_reader = pysam.Samfile(bam_in, "rb")
for current_sam in sam_reader.fetch(until_eof=True):
if previous_sam is None:
previous_sam = current_sam
continue
previous_type, current_type = mapping.get_pair_type(previous_sam, current_sam, self._get_ref_length_sam_pair(sam_reader, previous_sam, current_sam), self.max_insert, min_clip=self.min_clip)
for sam, sam_type in [(previous_sam, previous_type), (current_sam, current_type)]:
if sam_type == mapping.CAN_EXTEND_LEFT:
name = mapping.get_ref_name(sam, sam_reader)
clipped = mapping.soft_clipped(sam)[0]
self.contigs[name].add_left_kmer(common.decode(sam.seq[:clipped]))
elif sam_type == mapping.CAN_EXTEND_RIGHT:
name = mapping.get_ref_name(sam, sam_reader)
self.contigs[name].add_right_kmer(common.decode(sam.seq[sam.qend:]))
if out_prefix is not None and sam_type in keep_read_types:
if sam.is_read1:
print(mapping.sam_to_fasta(sam), file=fa_out1)
else:
print(mapping.sam_to_fasta(sam), file=fa_out2)
previous_sam = None
if out_prefix is not None:
pyfastaq.utils.close(fa_out1)
pyfastaq.utils.close(fa_out2)
total_bases_added = 0
for ctg in self.contigs:
left_length, right_length = self.contigs[ctg].extend(self.ext_min_cov, self.ext_min_ratio, self.ext_bases)
if self.verbose:
print(' extend contig ' + ctg, 'new_length:' + str(len(self.contigs[ctg])), 'added_left:' + str(left_length), 'added_right:' + str(right_length), sep='\t')
self.contig_lengths[ctg].append([len(self.contigs[ctg]), left_length, right_length])
total_bases_added += left_length + right_length
return total_bases_added
def test_get_ref_name(self):
'''Test get_ref_name'''
expected = ['ref'] * 14
for i in ([5,10,11]):
expected[i] = None
sam_reader = pysam.Samfile(os.path.join(data_dir, 'mapping_test.smalt.out.bam'), "rb")
i = 0
for sam in sam_reader.fetch(until_eof=True):
self.assertEqual(mapping.get_ref_name(sam, sam_reader), expected[i])
i += 1
def _get_ref_length(self, samfile, sam):
if sam.is_unmapped:
return None
else:
return len(self.contigs[mapping.get_ref_name(sam, samfile)])
def _get_ref_length(self, samfile, sam):
if sam.is_unmapped:
return None
else:
return len(self.contigs[mapping.get_ref_name(sam, samfile)])