if intron_counts[i] == 0
]
alignments_and_scores = [(alignment, [
int(tokens[5:]) for tokens in alignment if tokens[:5] == 'AS:i:'
][0]) for alignment in clipped_alignments]
alignments_and_scores.sort(key=lambda alignment: alignment[1],
reverse=True)
max_score = alignments_and_scores[0][1]
alignments_to_report = [
alignment for alignment, score in alignments_and_scores
if score == max_score
]
output_line_count += alignment_printer.print_alignment_data(
multiread_to_report(
alignments_to_report,
alignment_count_to_report=alignment_count_to_report,
seed=seed,
non_deterministic=non_deterministic,
weights=[1] * len(alignments_to_report)))
else:
# All alignments overlap introns
intron_alignments = [
alignments[i] for i in xrange(len(intron_counts))
if intron_counts[i] == min_intron_count
]
# Compute min coverage for alignments that are the same
alignment_dict = defaultdict(int)
for alignment in intron_alignments:
if alignment[:-1] not in alignment_dict:
alignment_dict[alignment[:-1]] = int(alignment[-1][5:])
else:
alignment_dict[alignment[:-1]] \
) if junction_counts[i] == 0]
alignments_and_scores = [(alignment, [int(tokens[5:])
for tokens in alignment
if tokens[:5] == 'AS:i:'][0])
for alignment in clipped_alignments]
alignments_and_scores.sort(key=lambda alignment: alignment[1],
reverse=True)
max_score = alignments_and_scores[0][1]
alignments_to_report = [alignment for alignment, score
in alignments_and_scores
if score == max_score]
output_line_count += alignment_printer.print_alignment_data(
multiread_to_report(
alignments_to_report,
alignment_count_to_report=alignment_count_to_report,
seed=seed,
non_deterministic=non_deterministic,
weights=[1]*len(alignments_to_report)
)
)
else:
# All alignments overlap junctions
junction_alignments = [alignments[i]
for i in xrange(len(junction_counts))
if junction_counts[i] == min_junction_count]
# Compute min coverage for alignments that are the same
alignment_dict = defaultdict(int)
for alignment in junction_alignments:
if alignment[:-1] not in alignment_dict:
alignment_dict[alignment[:-1]] = int(alignment[-1][5:])
else:
if not corrected_multiread:
'''This is effectively an unmapped read; write
corresponding SAM output.'''
if flag & 16:
seq_to_write = initial_multiread[0][9][::-1].translate(
reversed_complement_translation_table)
qual_to_write = initial_multiread[0][10][::-1]
else:
seq_to_write = initial_multiread[0][9]
qual_to_write = initial_multiread[0][10]
output_line_count \
+= alignment_printer.print_unmapped_read(
qname,
seq_to_write,
qual_to_write
)
continue
count = alignment_printer.print_alignment_data(
multiread_to_report(
corrected_multiread,
alignment_count_to_report=alignment_count_to_report,
seed=seed,
non_deterministic=non_deterministic,
tie_margin=args.tie_margin))
counter.add('output_lines', count)
output_line_count += count
print >>sys.stderr, 'DONE with compare_alignments.py; in/out=%d/%d; ' \
'time=%0.3f s' % (input_line_count, output_line_count,
time.time() - start_time)
if flag & 16:
seq_to_write = initial_multiread[0][9][::-1].translate(
reversed_complement_translation_table
)
qual_to_write = initial_multiread[0][10][::-1]
else:
seq_to_write = initial_multiread[0][9]
qual_to_write = initial_multiread[0][10]
output_line_count \
+= alignment_printer.print_unmapped_read(
qname,
seq_to_write,
qual_to_write
)
continue
count = alignment_printer.print_alignment_data(
multiread_to_report(
corrected_multiread,
alignment_count_to_report=alignment_count_to_report,
seed=seed,
non_deterministic=non_deterministic,
tie_margin=args.tie_margin
)
)
counter.add('output_lines', count)
output_line_count += count
print >>sys.stderr, 'DONE with compare_alignments.py; in/out=%d/%d; ' \
'time=%0.3f s' % (input_line_count, output_line_count,
time.time() - start_time)