go-gaf-inference.pl
go-gaf-inference.pl --infer go/ontology/obo_format_1_2/gene_ontology_ext.obo go/gene-associations/gene_association.sgd.gz
Performs inference upon a GAF (Gene Association File), generating ICs based on configurable criteria
Pass in --infer on the command line
Example:
go-gaf-inference.pl --infer --per-file go/ontology/obo_format_1_2/gene_ontology_ext.obo go/gene-associations/gene_association*.gz
generates IC BP annotations for MF annotations where a part_of link is asserted or can be inferred
TO BE DOCUMENTED
NOT YET IMPLEMENTED
Pass in --validate on the command line
http://wiki.geneontology.org/index.php/Category:Taxon
go-gaf-inference.pl --validate -i scratch/go-taxon/TaxonGOLinksFile.obo -i scratch/go-taxon/ncbitax-slim.obo -i scratch/go-taxon/UnionTerms.obo -i ontology/editors/gene_ontology_write.obo gene-associations/gene_association.goa_chicken.gz
Writes out taxonomically invalid annotations. Uses the correct semantics for union terms.
To install GOBO, copy and paste the appropriate command in to your terminal.
cpanm
cpanm GOBO
CPAN shell
perl -MCPAN -e shell install GOBO
For more information on module installation, please visit the detailed CPAN module installation guide.