Tools for handling gff files
Read the documentation
To install gff_toolkit simply run:
pip install gff_toolkit
To upgrade after a new version run:
pip install gff_toolkit --upgrade
#!/usr/bin/python
"""
Example on how to reformat manual annotations from Geneious to proper Gff
"""
__author__ = 'rensholmer'
import sys
import gff_toolkit as gt
def main(manual_file,author_name):
manual_gff = gt.parser(manual_file,filetype='manual',limit=dict(featuretype='CDS',source='Geneious'),author=author_name)
for gene in manual_gff.getitems(featuretype='gene'):
for subs in manual_gff.get_children(gene):
print subs.stringify().strip()
if __name__ == '__main__':
if len(sys.argv) == 3:
main(*sys.argv[1:])
else:
print 'Usage: python {0} <geneious manual annotation gff> <author name>'.format(sys.argv[0])