NAME

go-slimdown.pl

SYNOPSIS

 go-slimdown.pl -i go/ontology/gene_ontology.obo -s goslim_generic -o slimmed.obo

DESCRIPTION

# must supply these arguments... or else! -i || --ontology /path/to/<file_name> input file (ontology file) with path -s || --subset <subset_name> name of the subset to extract

 -o || --output /path/to/<file_name>     output file with path
  or
 -b || --basename /path/to/<file_name_containing_SLIM_NAME>

      specify a file name containing the text "SLIM_NAME", which will be
      substituted with the name of the subset
      e.g. -s goslim_goa -s goslim_yeast -b /temp/gene_ontology.SLIM_NAME.obo 
      would produce two files,
      /temp/gene_ontology.goslim_goa.obo and /temp/gene_ontology.goslim_yeast.obo

# optional args -c || --combined if more than one subset is specified, create a slim using terms from all of the subsets specified

 -v || --verbose                          prints various messages

        Given a file where certain terms are specified as being in subset S, this
        script will 'slim down' the file by removing terms not in the subset.
        
        Relationships between remaining terms are calculated by the inference engine.
        
        If the root nodes are not already in the subset, they are added to the graph.