Tools for handling gff files


Keywords
gff-toolkit, gff3, python
License
Other
Install
pip install gff_toolkit==0.1.12

Documentation

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gff_toolkit

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])