input_line_count += len(initial_multiread)
multiread = [
alignment for alignment in initial_multiread
if not (int(alignment[1]) & 4)
]
flag = int(initial_multiread[0][1])
if not multiread:
counter.add('unmapped')
# Write only the SAM output if the read was unmapped
output_line_count += alignment_printer.print_unmapped_read(
qname, initial_multiread[0][9], initial_multiread[0][10])
else:
'''Correct positions to match original reference's, correct
CIGARs, eliminate duplicates, and decide primary alignment.'''
try:
corrected_multiread = multiread_with_junctions(
multiread, stranded=args.stranded)
except:
print >> sys.stderr, ('Error encountered interpreting '
'multiread %s' % (multiread, ))
raise
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 \
def go(input_stream=sys.stdin, output_stream=sys.stdout, fudge=5,
stranded=False, verbose=False, max_refs=300, report_multiplier=1.2):
""" Emits junction combinations associated with reads.
Soft-clipped Bowtie 2 alignments of read sequences to the transcript
fragment index are used infer which cojunctions could possibly be
overlapped by reads. Then maximal cliques of the graph described in
the maximal_cliques() function are enumerated to obtain which
junction combinations could possibly be overlapped by reads.
input_stream: where to retrieve Bowtie 2 output
output_stream: where to emit exon and junction tuples; typically, this
is sys.stdout.
fudge: by how many bases to extend left and right extend sizes
to accommodate potential indels
stranded: True iff input reads are strand-specific; this affects
whether an output partition has a terminal '+' or '-' indicating
the sense strand. Further, if stranded is True, an alignment is
returned only if its strand agrees with the junction's strand.
verbose: True if alignments should occasionally be written to stderr.
max_refs: maximum number of reference sequences to enumerate per read;
if more are present, prioritize those sequences that overlap
the fewest junctions
report_multiplier: if verbose is True, the line number of an
alignment written to stderr increases exponentially with base
report_multiplier.
"""
output_line_count, next_report_line, i = 0, 0, 0
for (qname,), xpartition in xstream(input_stream, 1):
'''While labeled multireadlet, this list may end up simply a
unireadlet.'''
multiread = []
for tokens in xpartition:
flag = int(tokens[0])
if verbose and next_report_line == i:
print >>sys.stderr, \
'SAM output record %d: rdname="%s", flag=%d' % (i,
qname,
flag)
next_report_line = int((next_report_line + 1)
* report_multiplier + 1) - 1
i += 1
multiread.append((qname,) + tokens)
if flag & 4: continue
corrected_multiread = multiread_with_junctions(multiread,
stranded)
cojunctions, all_junctions = defaultdict(set), {}
for alignment in multiread_with_junctions(multiread, stranded):
cigar = alignment[5]
md = [field for field in alignment
if field[:5] == 'MD:Z:'][0][5:]
pos = int(alignment[3])
seq = alignment[9]
reversed_complement_seq = seq[::-1].translate(
_reversed_complement_translation_table
)
if seq < reversed_complement_seq:
seq_to_print = seq
else:
seq_to_print = reversed_complement_seq
seq_size = len(seq)
rname = alignment[2]
sense = [field for field in alignment
if field[:5] == 'XS:A:'][0][5:]
if (rname, sense) not in all_junctions:
all_junctions[(rname, sense)] = defaultdict(list)
_, _, junctions, _, _ = indels_junctions_exons_mismatches(
cigar, md, pos, seq,
junctions_only=True
)
cojunctions[(rname, sense)].add(
tuple([(junction[0], junction[1])
for junction in junctions])
)
for junction in junctions:
if (junction[0], junction[1]) \
not in all_junctions[(rname, sense)]:
all_junctions[(rname, sense)][(junction[0], junction[1])] \
= [junction[2], junction[3]]
else:
all_junctions[(rname, sense)][
(junction[0], junction[1])
][0] = max(all_junctions[(rname, sense)][
(junction[0], junction[1])
][0], junction[2])
all_junctions[(rname, sense)][
(junction[0], junction[1])
][1] = max(all_junctions[(rname, sense)][
(junction[0], junction[1])
][1], junction[3])
for rname, sense in all_junctions:
to_write = set()
for cojunction in selected_cojunctions(paths_from_cojunctions(
list(cojunctions[(rname, sense)]), span=(seq_size + fudge)
), max_refs=max_refs, seq=seq, rname=rname, sense=sense):
left_extend_size = all_junctions[(rname, sense)][
cojunction[0]
][0]
right_extend_size = all_junctions[(rname, sense)][
cojunction[-1]
][1]
to_write.add(('{rname}{sense}\t{starts}'
'\t{ends}\t{left_size}'
'\t{right_size}\t{seq}').format(
rname=rname,
sense=sense,
starts=','.join(
[str(junction[0])
for junction in cojunction]
),
ends=','.join(
[str(junction[1])
for junction in cojunction]
),
left_size=(left_extend_size
+ fudge),
right_size=(right_extend_size
+ fudge),
seq=seq_to_print
))
for line_to_write in to_write:
print line_to_write
output_line_count += 1
output_stream.flush()
print >>sys.stderr, ('cojunction_enum_delegate.py reports %d output lines.'
% output_line_count)
def go(input_stream=sys.stdin,
output_stream=sys.stdout,
fudge=5,
stranded=False,
verbose=False,
max_refs=300,
report_multiplier=1.2):
""" Emits junction combinations associated with reads.
Soft-clipped Bowtie 2 alignments of read sequences to the transcript
fragment index are used infer which cojunctions could possibly be
overlapped by reads. Then maximal cliques of the graph described in
the maximal_cliques() function are enumerated to obtain which
junction combinations could possibly be overlapped by reads.
input_stream: where to retrieve Bowtie 2 output
output_stream: where to emit exon and junction tuples; typically, this
is sys.stdout.
fudge: by how many bases to extend left and right extend sizes
to accommodate potential indels
stranded: True iff input reads are strand-specific; this affects
whether an output partition has a terminal '+' or '-' indicating
the sense strand. Further, if stranded is True, an alignment is
returned only if its strand agrees with the junction's strand.
verbose: True if alignments should occasionally be written to stderr.
max_refs: maximum number of reference sequences to enumerate per read;
if more are present, prioritize those sequences that overlap
the fewest junctions
report_multiplier: if verbose is True, the line number of an
alignment written to stderr increases exponentially with base
report_multiplier.
"""
output_line_count, next_report_line, i = 0, 0, 0
for (qname, ), xpartition in xstream(input_stream, 1):
'''While labeled multireadlet, this list may end up simply a
unireadlet.'''
multiread = []
for tokens in xpartition:
flag = int(tokens[0])
if verbose and next_report_line == i:
print >>sys.stderr, \
'SAM output record %d: rdname="%s", flag=%d' % (i,
qname,
flag)
next_report_line = int(
(next_report_line + 1) * report_multiplier + 1) - 1
i += 1
multiread.append((qname, ) + tokens)
if flag & 4: continue
cojunctions, all_junctions = defaultdict(set), {}
for alignment in multiread_with_junctions(multiread, stranded):
cigar = alignment[5]
md = [field for field in alignment if field[:5] == 'MD:Z:'][0][5:]
pos = int(alignment[3])
seq = alignment[9]
reversed_complement_seq = seq[::-1].translate(
_reversed_complement_translation_table)
if seq < reversed_complement_seq:
seq_to_print = seq
else:
seq_to_print = reversed_complement_seq
seq_size = len(seq)
rname = alignment[2]
sense = [field for field in alignment
if field[:5] == 'XS:A:'][0][5:]
if (rname, sense) not in all_junctions:
all_junctions[(rname, sense)] = defaultdict(list)
_, _, junctions, _, _ = indels_junctions_exons_mismatches(
cigar, md, pos, seq, junctions_only=True)
cojunctions[(rname, sense)].add(
tuple([(junction[0], junction[1]) for junction in junctions]))
for junction in junctions:
if (junction[0], junction[1]) \
not in all_junctions[(rname, sense)]:
all_junctions[(rname, sense)][(junction[0], junction[1])] \
= [junction[2], junction[3]]
else:
all_junctions[(rname, sense)][(
junction[0], junction[1])][0] = max(
all_junctions[(rname, sense)][(junction[0],
junction[1])][0],
junction[2])
all_junctions[(rname, sense)][(
junction[0], junction[1])][1] = max(
all_junctions[(rname, sense)][(junction[0],
junction[1])][1],
junction[3])
for rname, sense in all_junctions:
to_write = set()
for cojunction in selected_cojunctions(
paths_from_cojunctions(list(cojunctions[(rname, sense)]),
span=(seq_size + fudge)),
max_refs=max_refs,
seq=seq,
rname=rname,
sense=sense):
left_extend_size = all_junctions[(rname,
sense)][cojunction[0]][0]
right_extend_size = all_junctions[(rname,
sense)][cojunction[-1]][1]
to_write.add(
('{rname}{sense}\t{starts}'
'\t{ends}\t{left_size}'
'\t{right_size}\t{seq}').format(
rname=rname,
sense=sense,
starts=','.join(
[str(junction[0]) for junction in cojunction]),
ends=','.join(
[str(junction[1]) for junction in cojunction]),
left_size=(left_extend_size + fudge),
right_size=(right_extend_size + fudge),
seq=seq_to_print))
counter.add('paths_out', len(to_write))
for line_to_write in to_write:
print line_to_write
output_line_count += 1
output_stream.flush()
print >> sys.stderr, (
'cojunction_enum_delegate.py reports %d output lines.' %
output_line_count)
if not (int(alignment[1]) & 4)]
flag = int(initial_multiread[0][1])
if not multiread:
counter.add('unmapped')
# Write only the SAM output if the read was unmapped
output_line_count += alignment_printer.print_unmapped_read(
qname,
initial_multiread[0][9],
initial_multiread[0][10]
)
else:
'''Correct positions to match original reference's, correct
CIGARs, eliminate duplicates, and decide primary alignment.'''
try:
corrected_multiread = multiread_with_junctions(
multiread,
stranded=args.stranded
)
except:
print >>sys.stderr, ('Error encountered interpreting '
'multiread %s' % (multiread,))
raise
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]