Munges GFF3 files exported from Chado
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.
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].
pip3 install git+git://github.com/sanger-pathogens/gffmunger.git
Set up bioconda channel:
conda config --add channels bioconda
Install GFF munger:
conda install -c bioconda gffmunger
The test can be run from the top level directory:
./run_tests.sh
gffmunger [command1 ... commandN] [--input chado_export.gff3.gz] [--fasta chado_export.fasta] [--output webapollo_compatible.gff3] [--quiet|--verbose]
move_polypeptide_annot (default) transfers annotations from polypeptide features to the feature (e.g. mRNA) from which the polypeptide derives.
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.
GFF munger is free software, licensed under GPLv3.
Please report any issues to the issues page or email [email protected].