Processing steps to map gene ontologies onto a GOslim
First, download go.obo from http://geneontology.org/ontology/go.obo and save as data/go.obo
Save the annotation file you want to slim down (contig name followed by tab sep GO terms) in data/
Save the GOslim you want in goslim
directory
- Run
1_pickle.obo/py
to pickle go.obo into go.p
Usage is python 1_pickle.obo.py - Run
2_parse_go_obo.py
to properly index go.p file
Usage is python 2_parse_go_out.py - Run
3_go2gaf.py
to generate gene association file
Usage is python 3_go2gaf.py data/inFile data/go.p > data/outFile.gaf
inFile is full GO annotation file - Run
4_map2slim.sh
to get slim terms using owltools
Usage is 4_map2slim.sh annotateSNPs.R
does some analysis with output slim file