######################### ABOUT #########################

MiniGFF is a set of Python tools for extracting minimal GFF files from a Chado database. These files do not have any annotation, their purpose (currently) is for use by JBrowse, which doesn't necessarily make use of all the annotations.

######################### CONFIGURATION #########################

To run you must first rename the config.ini.default to config.ini and then edit the file to match your Chado installation.

Depends on the python psycopg2 library.

######################### EXECUTION #########################

gff.py

You run this by doing

python gff.py -featureUniqueName Lbr.chr3 

where -featureUniqueName is a top-level Chado feature (in this case LBraziliensis, chromosome 3).

gff_organism.py

For a given organism, you can run

python gff_organism.py -organism Lbraziliensis -savePath test

where the -organism parameter refers to its common_name, and the option -savePath parameter refers to a path on your system where you want the files dumped out. If you omit -savePath, it will dump everything to standard out.

gff_organisms.py

Will return features for a list of organisms, if you supply the -organisms parameter

python gff_organisms.py -savePath test -organisms Sjaponicum Saureus_MSSA476 Nmeningitidis

or will attempt to export for all the organisms in the database, if -organisms is ommitted

python gff_organisms.py -savePath test

Please note that -savePath is not optional here.