def to_gtf_features(self, source=None):
if source is None:
source = 'source'
# transcript feature
f = GTFFeature()
f.seqid = self.chrom
f.source = source
f.feature_type = 'transcript'
f.start = self.start
f.end = self.end
f.score = 1000.0
f.strand = self.strand
f.phase = '.'
f.attrs = self.attrs.copy()
features = [f]
# exon features
for i,e in enumerate(self.exons):
start,end = e
f = GTFFeature()
f.seqid = self.chrom
f.source = source
f.feature_type = 'exon'
f.start = start
f.end = end
f.score = 1000.0
f.strand = self.strand
f.phase = '.'
f.attrs = self.attrs.copy()
f.attrs["exon_number"] = i
features.append(f)
return features
def get_gtf_features(chrom, strand, exons, locus_id, gene_id, tss_id,
transcript_id, score, frac):
tx_start = exons[0].start
tx_end = exons[-1].end
strand_str = strand_int_to_str(strand)
attr_dict = {'locus_id': locus_id,
'gene_id': gene_id,
'tss_id': tss_id,
'transcript_id': transcript_id}
f = GTFFeature()
f.seqid = chrom
f.source = 'assemblyline'
f.feature_type = 'transcript'
f.start = tx_start
f.end = tx_end
f.score = 1000.0 * int(round(frac))
f.strand = strand_str
f.phase = '.'
f.attrs = {'score': '%.3f' % score,
'frac': '%.3f' % frac}
f.attrs.update(attr_dict)
yield f
for i,e in enumerate(exons):
f = GTFFeature()
f.seqid = chrom
f.source = 'assemblyline'
f.feature_type = 'exon'
f.start = e.start
f.end = e.end
f.score = int(round(frac))
f.strand = strand_str
f.phase = '.'
f.attrs = {'exon_number': i+1}
f.attrs.update(attr_dict)
yield f
def to_gtf_features(self, source=None):
if source is None:
source = 'source'
# transcript feature
f = GTFFeature()
f.seqid = self.chrom
f.source = source
f.feature_type = 'transcript'
f.start = self.start
f.end = self.end
f.score = 1000.0
f.strand = self.strand
f.phase = '.'
f.attrs = self.attrs.copy()
features = [f]
# exon features
for i, e in enumerate(self.exons):
start, end = e
f = GTFFeature()
f.seqid = self.chrom
f.source = source
f.feature_type = 'exon'
f.start = start
f.end = end
f.score = 1000.0
f.strand = self.strand
f.phase = '.'
f.attrs = self.attrs.copy()
f.attrs["exon_number"] = i
features.append(f)
return features
def get_gtf_features(chrom, strand, exons, locus_id, gene_id, tss_id, transcript_id, score, frac):
tx_start = exons[0].start
tx_end = exons[-1].end
strand_str = strand_int_to_str(strand)
attr_dict = {"locus_id": locus_id, "gene_id": gene_id, "tss_id": tss_id, "transcript_id": transcript_id}
f = GTFFeature()
f.seqid = chrom
f.source = "assemblyline"
f.feature_type = "transcript"
f.start = tx_start
f.end = tx_end
f.score = 1000.0 * int(round(frac))
f.strand = strand_str
f.phase = "."
f.attrs = {"score": "%.3f" % score, "frac": "%.3f" % frac}
f.attrs.update(attr_dict)
yield f
for i, e in enumerate(exons):
f = GTFFeature()
f.seqid = chrom
f.source = "assemblyline"
f.feature_type = "exon"
f.start = e.start
f.end = e.end
f.score = int(round(frac))
f.strand = strand_str
f.phase = "."
f.attrs = {"exon_number": i + 1}
f.attrs.update(attr_dict)
yield f
def get_gtf_features(chrom, strand, exons, locus_id, gene_id, tss_id,
transcript_id, score, frac):
tx_start = exons[0].start
tx_end = exons[-1].end
strand_str = strand_int_to_str(strand)
attr_dict = {'locus_id': locus_id,
'gene_id': gene_id,
'tss_id': tss_id,
'transcript_id': transcript_id}
f = GTFFeature()
f.seqid = chrom
f.source = 'assemblyline'
f.feature_type = 'transcript'
f.start = tx_start
f.end = tx_end
f.score = 1000.0 * int(round(frac))
f.strand = strand_str
f.phase = '.'
f.attrs = {'score': '%.3f' % score,
'frac': '%.3f' % frac}
f.attrs.update(attr_dict)
yield f
for i,e in enumerate(exons):
f = GTFFeature()
f.seqid = chrom
f.source = 'assemblyline'
f.feature_type = 'exon'
f.start = e.start
f.end = e.end
f.score = int(round(frac))
f.strand = strand_str
f.phase = '.'
f.attrs = {'exon_number': i+1}
f.attrs.update(attr_dict)
yield f
def get_cds_features(gtf_file):
cds = collections.defaultdict(lambda: set())
i = 0
for f in GTFFeature.parse(open(gtf_file)):
if f.feature_type == "CDS":
cds[f.seqid].add((f.start, f.end, f.strand))
i += 1
if (i % 100000) == 0:
logging.debug("Parsed %d features" % (i))
logging.debug("Returning CDS transcripts")
t_id = 1
for chrom in sorted(cds):
for start, end, strand in sorted(cds[chrom]):
for feature_type in ('transcript', 'exon'):
f = GTFFeature()
f.seqid = chrom
f.source = 'cds'
f.feature_type = feature_type
f.start = start
f.end = end
f.score = 0
f.strand = strand
f.phase = '.'
f.attrs = {'cds': 1, 'transcript_id': 'CDS%08d' % (t_id)}
yield f
t_id += 1
def add_gtf_file(gtf_file, outfh, is_ref):
refval = '1' if is_ref else '0'
for chrom, transcript_dict, exon_dict in _parse_gtf_by_chrom(gtf_file):
logging.debug("\tfinished chrom %s %d features" %
(chrom, len(exon_dict)))
# output reference transcripts
for t_id, features in exon_dict.iteritems():
# sort features (exons) by start position
features.sort(key=operator.attrgetter('start'))
# annotate exons as reference features
for f in features:
f.attrs[GTFAttr.REF] = refval
print >> outfh, str(f)
# transcript feature
if t_id in transcript_dict:
f = transcript_dict[t_id]
else:
f = GTFFeature()
f.seqid = features[0].seqid
f.source = features[0].source
f.feature_type = 'transcript'
f.start = features[0].start
f.end = features[-1].end
f.score = features[0].score
f.strand = features[0].strand
f.phase = '.'
f.attrs = features[0].attrs.copy()
if "exon_number" in f.attrs:
del f.attrs["exon_number"]
f.attrs[GTFAttr.REF] = refval
print >> outfh, str(f)
def gtf_add_transcript_features(gtf_file, outfh):
transcript_dict = collections.defaultdict(lambda: [])
for feature in GTFFeature.parse(open(gtf_file)):
if feature.feature_type != "exon":
continue
t_id = feature.attrs[GTFAttr.TRANSCRIPT_ID]
transcript_dict[t_id].append(feature)
# output reference transcripts
for t_id, features in transcript_dict.iteritems():
# sort features (exons) by start position
features.sort(key=operator.attrgetter('start'))
# transcript feature
f = GTFFeature()
f.seqid = features[0].seqid
f.source = features[0].source
f.feature_type = 'transcript'
f.start = features[0].start
f.end = features[-1].end
f.score = features[0].score
f.strand = features[0].strand
f.phase = '.'
f.attrs = features[0].attrs.copy()
if "exon_number" in f.attrs:
del f.attrs["exon_number"]
#f.attrs[GTFAttr.REF] = '1'
print >>outfh, str(f)
# annotate exons as reference features
for f in features:
#f.attrs[GTFAttr.REF] = '1'
print >>outfh, str(f)
def add_gtf_file(gtf_file, outfh, is_ref, sample_id=None):
refval = '1' if is_ref else '0'
for chrom, transcript_dict, exon_dict in _parse_gtf_by_chrom(gtf_file):
logging.debug("\tfinished chrom %s %d features" % (chrom, len(exon_dict)))
# output reference transcripts
for t_id, features in exon_dict.iteritems():
# sort features (exons) by start position
features.sort(key=operator.attrgetter('start'))
# annotate exons as reference features
for f in features:
f.attrs[GTFAttr.REF] = refval
print >>outfh, str(f)
# transcript feature
if t_id in transcript_dict:
f = transcript_dict[t_id]
else:
f = GTFFeature()
f.seqid = features[0].seqid
f.source = features[0].source
f.feature_type = 'transcript'
f.start = features[0].start
f.end = features[-1].end
f.score = features[0].score
f.strand = features[0].strand
f.phase = '.'
f.attrs = features[0].attrs.copy()
if "exon_number" in f.attrs:
del f.attrs["exon_number"]
f.attrs[GTFAttr.REF] = refval
if sample_id is not None:
f.attrs[GTFAttr.SAMPLE_ID] = sample_id
print >>outfh, str(f)
def get_cds_features(gtf_file):
cds = collections.defaultdict(lambda: set())
i = 0
for f in GTFFeature.parse(open(gtf_file)):
if f.feature_type == "CDS":
cds[f.seqid].add((f.start, f.end, f.strand))
i += 1
if (i % 100000) == 0:
logging.debug("Parsed %d features" % (i))
logging.debug("Returning CDS transcripts")
t_id = 1
for chrom in sorted(cds):
for start,end,strand in sorted(cds[chrom]):
for feature_type in ('transcript', 'exon'):
f = GTFFeature()
f.seqid = chrom
f.source = 'cds'
f.feature_type = feature_type
f.start = start
f.end = end
f.score = 0
f.strand = strand
f.phase = '.'
f.attrs = {'cds': 1,
'transcript_id': 'CDS%08d' % (t_id)}
yield f
t_id += 1
def main():
logging.basicConfig(level=logging.DEBUG,
format="%(asctime)s - %(name)s - %(levelname)s - %(message)s")
parser = argparse.ArgumentParser()
parser.add_argument("--source", dest="source", default='bed_to_gtf')
parser.add_argument("bed_file")
args = parser.parse_args()
bed_file = args.bed_file
source = args.source
for x in BEDFeature.parse(open(bed_file)):
f = GTFFeature()
f.seqid = x.chrom
f.source = source
f.feature_type = 'transcript'
f.start = x.tx_start
f.end = x.tx_end
f.score = x.score
f.strand = x.strand
f.phase = '.'
f.attrs = {'transcript_id': x.name,
'gene_id': x.name}
features = [f]
for i,e in enumerate(x.exons):
start, end = e
f = GTFFeature()
f.seqid = x.chrom
f.source = source
f.feature_type = 'exon'
f.start = start
f.end = end
f.score = x.score
f.strand = x.strand
f.phase = '.'
f.attrs = dict(features[0].attrs)
f.attrs["exon_number"] = i
features.append(f)
for f in features:
print str(f)
def main():
logging.basicConfig(
level=logging.DEBUG,
format="%(asctime)s - %(name)s - %(levelname)s - %(message)s")
parser = argparse.ArgumentParser()
parser.add_argument("--source", dest="source", default='bed_to_gtf')
parser.add_argument("bed_file")
args = parser.parse_args()
bed_file = args.bed_file
source = args.source
for x in BEDFeature.parse(open(bed_file)):
f = GTFFeature()
f.seqid = x.chrom
f.source = source
f.feature_type = 'transcript'
f.start = x.tx_start
f.end = x.tx_end
f.score = x.score
f.strand = x.strand
f.phase = '.'
f.attrs = {'transcript_id': x.name, 'gene_id': x.name}
features = [f]
for i, e in enumerate(x.exons):
start, end = e
f = GTFFeature()
f.seqid = x.chrom
f.source = source
f.feature_type = 'exon'
f.start = start
f.end = end
f.score = x.score
f.strand = x.strand
f.phase = '.'
f.attrs = dict(features[0].attrs)
f.attrs["exon_number"] = i
features.append(f)
for f in features:
print str(f)
def make_transcript_feature(exon_features):
f = GTFFeature()
f.seqid = exon_features[0].seqid
f.source = exon_features[0].source
f.feature_type = 'transcript'
f.start = exon_features[0].start
f.end = exon_features[-1].end
f.score = exon_features[0].score
f.strand = exon_features[0].strand
f.phase = '.'
f.attrs = exon_features[0].attrs.copy()
if "exon_number" in f.attrs:
del f.attrs["exon_number"]
return f