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, 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)
