def process_Genbank( filename, org_num, refseq ):
#extracts 'CDS', 'tRNA', 'rRNA' features from genbank file
features = get_bed_from_genbank( filename, refseq, ['CDS', 'tRNA', 'rRNA'] )
for feature in features.keys():
feature_file = open( os.path.join( os.path.split( filename )[0], "%s.%s.bed" % ( refseq, feature ) ), 'wb+' )
feature_file.write( '\n'.join( features[feature] ) )
feature_file.close()
print "Genbank extraction finished for chrom:", refseq, "file:", filename
def process_Genbank( filename, org_num, refseq ):
# extracts 'CDS', 'tRNA', 'rRNA' features from genbank file
features = get_bed_from_genbank( filename, refseq, ['CDS', 'tRNA', 'rRNA'] )
for feature in features.keys():
feature_file = open( os.path.join( os.path.split( filename )[0], "%s.%s.bed" % ( refseq, feature ) ), 'wb+' )
feature_file.write( '\n'.join( features[feature] ) )
feature_file.close()
print "Genbank extraction finished for chrom:", refseq, "file:", filename
def process_Genbank(filename, org_num, refseq):
# extracts 'CDS', 'tRNA', 'rRNA' features from genbank file
features = get_bed_from_genbank(filename, refseq, ['CDS', 'tRNA', 'rRNA'])
for feature, values in features.items():
feature_file = open(
os.path.join(
os.path.split(filename)[0], f"{refseq}.{feature}.bed"), 'wb+')
feature_file.write('\n'.join(values))
feature_file.close()
print("Genbank extraction finished for chrom:", refseq, "file:", filename)