https://github.com/holmrenser/gff_toolkit

tools for handling gff files
https://github.com/holmrenser/gff_toolkit

gff-toolkit gff3 python

Last synced: about 1 month ago
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tools for handling gff files

• Host: GitHub
• URL: https://github.com/holmrenser/gff_toolkit
• Owner: holmrenser
• License: mit
• Created: 2015-08-18T08:28:51.000Z (over 9 years ago)
• Default Branch: master
• Last Pushed: 2016-12-22T11:09:11.000Z (about 8 years ago)
• Last Synced: 2024-11-19T03:33:30.527Z (about 2 months ago)
• Topics: gff-toolkit, gff3, python
• Language: Python
• Size: 66.4 KB
• Stars: 1
• Watchers: 2
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: license.txt

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# gff_toolkit

Tools for handling gff files

Read the [documentation](http://gff-toolkit.readthedocs.org/)

To install gff_toolkit simply run:

```pip install gff_toolkit```

To upgrade after a new version run:

```pip install gff_toolkit --upgrade```

```python

#!/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}  '.format(sys.argv[0])

```