def read_gff(self, line, prefix): # Takes prefix b/c reader returns comments, invalids, ignored # and this method writes them to output files # That's kind of messy gffreader = GFFReader() reader = open(line, 'rb') genes, comments, invalids, ignored = gffreader.read_file(reader) for gene in genes: self.add_gene(gene) # Write comments, invalid lines and ignored features with open(prefix + "/genome.comments.gff", 'w') as comments_file: for comment in comments: comments_file.write(comment) with open(prefix + "/genome.invalid.gff", 'w') as invalid_file: for invalid in invalids: invalid_file.write(invalid) with open(prefix + "/genome.ignored.gff", 'w') as ignored_file: for item in ignored: ignored_file.write(item)
def read_gff(self, line): gffreader = GFFReader() reader = open(line, 'rb') genes = gffreader.read_file(reader) for gene in genes: self.add_gene(gene)