def from_gtf(f):
'''GTF.Feature object to Transfrag'''
return Transfrag(chrom=f.seqid,
strand=Strand.from_gtf(f.strand),
_id=f.attrs[GTF.Attr.TRANSCRIPT_ID],
sample_id=f.attrs.get(GTF.Attr.SAMPLE_ID, None),
expr=float(f.attrs.get(GTF.Attr.EXPR, 0.0)),
is_ref=bool(int(f.attrs.get(GTF.Attr.REF, '0'))),
exons=None)
def from_gtf(f):
'''GTF.Feature object to Transfrag'''
return Transfrag(chrom=f.seqid,
strand=Strand.from_gtf(f.strand),
_id=f.attrs[GTF.Attr.TRANSCRIPT_ID],
sample_id=f.attrs.get(GTF.Attr.SAMPLE_ID, None),
expr=float(f.attrs.get(GTF.Attr.EXPR, 0.0)),
is_ref=bool(int(f.attrs.get(GTF.Attr.REF, '0'))),
exons=None)
def parse_gtf(gtf_iter, sample_id, gtf_expr_attr, is_ref):
'''
returns list of Transfrag objects
'''
t_dict = collections.OrderedDict()
total_expr = 0.0
cur_t_id = 1
for gtf_line in gtf_iter:
if not gtf_line:
continue
if not gtf_line.strip():
continue
if gtf_line.startswith("#"):
continue
f = GTF.Feature.from_str(gtf_line)
if f.feature == 'transcript':
t_id = f.attrs[GTF.Attr.TRANSCRIPT_ID]
if t_id in t_dict:
raise GTFError("Transcript '%s' duplicate detected" % t_id)
# rename transcript id
new_t_id = "%s.%d" % (sample_id, cur_t_id)
cur_t_id += 1
# parse expression
if is_ref:
expr = 0.0
else:
if gtf_expr_attr not in f.attrs:
raise GTFError("GTF expression attribute '%s' not found" %
(gtf_expr_attr))
expr = float(f.attrs[gtf_expr_attr])
total_expr += expr
# create transfrag
t = Transfrag(chrom=f.seqid,
strand=Strand.from_gtf(f.strand),
_id=new_t_id,
expr=float(expr),
is_ref=is_ref,
exons=None)
t_dict[t_id] = t
elif f.feature == 'exon':
t_id = f.attrs[GTF.Attr.TRANSCRIPT_ID]
if t_id not in t_dict:
logging.error('Feature: "%s"' % str(f))
raise GTFError("Transcript '%s' exon feature appeared in "
"gtf file prior to transcript feature" %
t_id)
t = t_dict[t_id]
t.exons.append(Exon(f.start, f.end))
return t_dict.values(), total_expr
def parse_gtf(gtf_iter, sample_id, gtf_expr_attr, is_ref):
'''
returns list of Transfrag objects
'''
t_dict = collections.OrderedDict()
total_expr = 0.0
cur_t_id = 1
for gtf_line in gtf_iter:
if not gtf_line:
continue
if not gtf_line.strip():
continue
if gtf_line.startswith("#"):
continue
f = GTF.Feature.from_str(gtf_line)
if f.feature == 'transcript':
t_id = f.attrs[GTF.Attr.TRANSCRIPT_ID]
if t_id in t_dict:
raise GTFError("Transcript '%s' duplicate detected" % t_id)
# rename transcript id
new_t_id = "%s.%d" % (sample_id, cur_t_id)
cur_t_id += 1
# parse expression
if is_ref:
expr = 0.0
else:
if gtf_expr_attr not in f.attrs:
raise GTFError("GTF expression attribute '%s' not found" %
(gtf_expr_attr))
expr = float(f.attrs[gtf_expr_attr])
total_expr += expr
# create transfrag
t = Transfrag(chrom=f.seqid,
strand=Strand.from_gtf(f.strand),
_id=new_t_id,
expr=float(expr),
is_ref=is_ref,
exons=None)
t_dict[t_id] = t
elif f.feature == 'exon':
t_id = f.attrs[GTF.Attr.TRANSCRIPT_ID]
if t_id not in t_dict:
logging.error('Feature: "%s"' % str(f))
raise GTFError("Transcript '%s' exon feature appeared in "
"gtf file prior to transcript feature" % t_id)
t = t_dict[t_id]
t.exons.append(Exon(f.start, f.end))
return t_dict.values(), total_expr