obo2flat

The obo2flat utility converts an OBO file to one or more GO Flat Files.

obo2flat [options] <inputfile1> <inputfile2> ... <inputfileN> 

The command line parameters are:

Options

IO Switches:

Graph Rearrangement (required):

Optional Switches:

Presets:

obo2flat -cr GO:0003673 Gene_Ontology \
-co GO:0003674 GO:0008369 'obsolete molecular function' \
-co GO:0005575 GO:0008370 'obsolete cellular component' \
-co GO:0008150 GO:0008371 'obsolete biological process' \
-mapobs GO:0003674 function \
-mapobs GO:0005575 component \
-mapobs GO:0008150 process \
-defaultobs GO:0003674 \
-rootreltype GO:0003674 part_of \
-rootreltype GO:0005575 part_of \
-rootreltype GO:0008150 part_of \
-symbol part_of '>' \
-symbol is_a '%' \
-o GO:0003674 biological_process_output_file \
-o GO:0005575 cellular_component_output_file \
-o GO:0008150 molecular_function_output_file \
-def definitions_output_file

Other switches:

Also see Java Options on the Command-line

Example:

To convert an OBO file at ~/cvs/go/ontology/gene_ontology.obo into GO compatible flat files:

obo2flat --gopresets ~/cvs/go/ontology/process.ontology ~/cvs/go/ontology/component.ontology ~/cvs/go/ontology/function.ontology ~/cvs/go/docs/GO.defs.current ~/cvs/go/ontology/input.obo