trstickland/gffmunger repository overview

⁠GFF munger

Munges GFF3 files exported from Chado

⁠Contents

• Introduction⁠
• Installation⁠
  • Using pip3⁠
  • Conda⁠
  • Debian/Ubuntu (Trusty/Xenial)⁠
  • Running the tests⁠
• Usage⁠
• License⁠
• Feedback/Issues⁠

⁠Introduction

Munges GFF3 files exported from Chado (http://www.gmod.org/⁠) database to make them suitable for loading into WebApollo.

Currently supports very few functions, but provides a possible framework for additional functionality.

⁠Installation

There are a number of ways to install GFF munger and details are provided below. If you encounter an issue when installing GFF munger please contact your local system administrator. If you encounter a bug please log it here⁠ or email us at [email protected]⁠.

⁠Using pip3

pip3 install git+git://github.com/sanger-pathogens/gffmunger.git

⁠Conda

Set up bioconda channel:

conda config --add channels bioconda

Install GFF munger:

conda install -c bioconda gffmunger

⁠Running the tests

The test can be run from the top level directory:

./run_tests.sh

⁠Synopsis

gffmunger [command1 ... commandN] [--input chado_export.gff3.gz] [--fasta chado_export.fasta] [--output webapollo_compatible.gff3] [--quiet|--verbose]

⁠Commands

move_polypeptide_annot (default) transfers annotations from polypeptide features to the feature (e.g. mRNA) from which the polypeptide derives.

⁠Input/output options

Without --input, will read from standard input; without --output, will write new GFF3 to standard output. If --fasta is not used, then will read FASTA data (if present) from the input GFF3 file.

⁠License

GFF munger is free software, licensed under GPLv3⁠.

⁠Feedback/Issues

Please report any issues to the issues page⁠ or email [email protected]⁠.