def run(self):
spans = collections.defaultdict(list)
for item in legion.parallel_imap(self._load_bam, self.filenames):
for key,value in item.items():
spans[key].extend(value)
grace.status('Calling peaks')
f = open(self.prefix+'.gff', 'wb')
annotation.write_gff3_header(f)
n = 0
for (rname, strand), span_list in spans.items():
depth = [ 0.0 ] * (1+max( item[1] for item in span_list ))
for start, end in span_list:
depth[start] += 1.0
depth[end] -= 1.0
for i in xrange(1,len(depth)):
depth[i] += depth[i-1]
for start, end in self._find_spans(depth):
if end-self.lap-start <= 0: continue
n += 1
id = 'peak%d' % n
ann = annotation.Annotation()
ann.source = 'nesoni'
ann.type = self.type
ann.seqid = rname
ann.start = start
ann.end = end - self.lap
ann.strand = strand
ann.score = None
ann.phase = None
ann.attr = {
'id' : id,
'color' : '#00ff00' if strand > 0 else '#0000ff' if strand < 0 else '#008080',
}
print >> f, ann.as_gff()
f.flush()
f.close()
self.log.datum('-','called peaks',n)
grace.status('')
def run(self):
assert self.what in ('fragment','5prime','3prime'), 'Unknown option for --what.'
#assert self.moderation > 0.0, '--moderation must be greater than zero.'
#assert self.power > 0.0, '--power must be greater than zero.'
#assert self.width_power >= 1.0, '--width-power must be greater than or equal to one.'
#if self.filter == 'poly':
# use_bam_filename = 'alignments.bam'
# use_only_top = True
# use_only_monogamous = False
# expect_multiple_alignments = True
#elif self.filter == 'mono':
# use_bam_filename = 'alignments.bam'
# use_only_top = True
# use_only_monogamous = True
# expect_multiple_alignments = True
#else:
# assert self.filter == 'existing', 'Unrecognized filtering mode'
# use_bam_filename = 'alignments_filtered.bam'
# use_only_top = False
# use_only_monogamous = False
# expect_multiple_alignments = False
spans = collections.defaultdict(list)
for item in legion.parallel_imap(self._load_bam, self.filenames):
for key,value in item.items():
spans[key].extend(value)
#for i, filename in enumerate(self.filenames):
# if os.path.isdir(filename):
# filename = os.path.join(filename, use_bam_filename)
#
# n = 0
# for read_name, fragment_alignments, unmapped in \
# sam.bam_iter_fragments(
# filename,
# 'Scanning sample %d of %d' % (i+1,len(self.filenames))):
# if not fragment_alignments:
# continue
#
# if use_only_top:
# fragment_scores = [ sum( al.get_AS() for al in item ) for item in fragment_alignments ]
# best_score = max(fragment_scores)
# fragment_alignments = [
# item
# for item, score in zip(fragment_alignments, fragment_scores)
# if score >= best_score ]
#
# for alignments in fragment_alignments:
# if self.strand_specific:
# strand = -1 if alignments[0].flag&sam.FLAG_REVERSE else 1
# else:
# strand = 0
#
# start = min(item.pos-1 for item in alignments)
# end = max(item.pos+item.length-1 for item in alignments)
# if end-start <= self.trim*2: continue
#
# rname = alignments[0].rname
# spans[(rname, strand)].append((start+self.trim,end-self.trim))
#
# n += 1
# #if n > 100000: break
#
#if self.deduplicate:
# for key in spans:
# spans[key] = list(set(spans[key]))
grace.status('Calling peaks')
f = open(self.prefix+'.gff', 'wb')
annotation.write_gff3_header(f)
n = 0
for (rname, strand), span_list in spans.items():
depth = [ 0.0 ] * (1+max( item[1] for item in span_list ))
for start, end in span_list:
depth[start] += 1.0
depth[end] -= 1.0
if self.crosstalk and strand and (rname,-strand) in spans:
for start, end in spans[(rname,-strand)]:
if start < len(depth): depth[start] -= self.crosstalk
if end < len(depth): depth[end] += self.crosstalk
for i in xrange(1,len(depth)):
depth[i] += depth[i-1]
if self.crosstalk:
for i in xrange(len(depth)):
depth[i] = max(0.0,depth[i])
#import pylab
#pylab.plot(depth)
for start, end in self._find_spans(depth):
#pylab.axvspan(start-0.5,end-0.5,alpha=0.25)
if end-self.lap-start <= 0: continue
n += 1
id = 'peak%d' % n
#if strand == -1:
# id = '%s-%d..%d' % (rname,start,end+1)
#elif strand == 0:
# id = '%s.%d..%d' % (rname,start+1,end)
#else:
# id = '%s+%d..%d' % (rname,start+1,end)
ann = annotation.Annotation()
ann.source = 'nesoni'
ann.type = self.type
ann.seqid = rname
ann.start = start
ann.end = end - self.lap
ann.strand = strand
ann.score = None
ann.phase = None
ann.attr = {
'id' : id,
'color' : '#00ff00' if strand > 0 else '#0000ff' if strand < 0 else '#008080',
}
print >> f, ann.as_gff()
f.flush()
#pylab.show()
f.close()
self.log.datum('-','called peaks',n)
grace.status('')
