def get_records( genome,gff,verbose ):
"""Return list of records from genome with
annotations from annotation file.
GFF is 1-base; inclusive so
start-1, end the same
"""
if verbose:
sys.stderr.write( "Generating annotations for genome...\n" )
#load annotation
if gff.endswith(".gff"):
contig2coding,trans2exon = load_sgd_gff( gff )
else:
contig2coding,trans2exon = parse_gtf( gff )
records = []
for r in SeqIO.parse( open(genome),"fasta" ):
t = "CDS"
if r.id in contig2coding:
for s,e,name,stnd,score in contig2coding[r.id]:
strand = 1
if stnd == "-":
strand = -1
r.features.append( SeqFeature(FeatureLocation(s-1,e),type=t,strand=strand,id=name ) )
elif verbose:
sys.stderr.write( " Warning: no annotation for %s\n" % r.id )
#add to list
records.append( r )
return records
def get_records( genome,gff,verbose ):
"""Return list of records from genome with
annotations from annotation file.
GFF is 1-base; inclusive so
start-1, end the same
"""
if verbose:
sys.stderr.write( "Generating annotations for genome...\n" )
#load annotation
if gff.endswith(".gff"):
contig2coding,trans2exon = load_sgd_gff( gff )
else:
contig2coding,trans2exon = parse_gtf( gff )
records = []
for r in SeqIO.parse( open(genome),"fasta" ):
t = "CDS"
if r.id in contig2coding:
for s,e,name,stnd,score in contig2coding[r.id]:
strand = 1
if stnd == "-":
strand = -1
r.features.append( SeqFeature(FeatureLocation(s-1,e),type=t,strand=strand,id=name ) )
elif verbose:
sys.stderr.write( " Warning: no annotation for %s\n" % r.id )
#add to list
records.append( r )
return records