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ABOUT
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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.

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CONFIGURATION
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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. 



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EXECUTION
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#### 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.