/map2slim

GOslim annotation

Primary LanguageOpenEdge ABL

go_annotation

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

  1. Run 1_pickle.obo/py to pickle go.obo into go.p
    Usage is python 1_pickle.obo.py
  2. Run 2_parse_go_obo.py to properly index go.p file
    Usage is python 2_parse_go_out.py
  3. 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
  4. Run 4_map2slim.sh to get slim terms using owltools
    Usage is 4_map2slim.sh
  5. annotateSNPs.R does some analysis with output slim file