standalone perl scripts for hacking obo files
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GOBO
bin
t
templates
README
add-ontology-tag.pl
biomart-fetch.pl
gaf-grep.pl
gaf2gpx.pl
generate-daily-files.pl
generate-owl-catalog.pl
get-gafs.pl
go-enrichment-runner.pl
gpx2gaf.pl
mesh2obo.pl
obo-add-comments.pl
obo-add-data-version.pl
obo-add-def-xrefs.pl
obo-add-defs.pl
obo-add-relationships-from-xps.pl
obo-add-remark.pl
obo-assign-ids.pl
obo-cat.pl
obo-check-xps.pl
obo-cvs-log-and-diff.pl
obo-def-differ.pl
obo-extract-referenced-stanzas.pl
obo-extract-xrefs.pl
obo-fetch-remote-ontology.pl
obo-filter-external.pl
obo-filter-relationships.pl
obo-filter-tags.pl
obo-filter-unused.pl
obo-grep.pl
obo-ids-to-obolibrary-uris.pl
obo-map-annotations.pl
obo-map-ids.pl
obo-merge-equivalent-terms.pl
obo-merge-for-visualization.pl
obo-merge-tags.pl
obo-metadata-to-owl.pl
obo-multi-merge.pl
obo-obsoletify.pl
obo-order-tags.pl
obo-promote-dbxref-to-intersection.pl
obo-remove-case-sensitive-synonyms.pl
obo-rename-subsetdefs.pl
obo-sed.pl
obo-simple-diff.pl
obo-simple-merge.pl
obo-skip-header.pl
obo-split.pl
obo-strip.pl
obo-subtract.pl
obo-syntax-highlight-in-html.pl
obodata.pl
obolibrary-uris-to-obo-ids.pl
process-RefGenomeOrthologs.pl
tbl2obo.pl
tbl2obo_altid.pl
tbl2obolinks.pl
windforward-svn.pl

README

A collection of ad-hoc scripts for hacking obo format files.

These scripts are all standalone - no installation of perl modules is
required. As such, they rely on hacky quick and dirty parsing
techniques rather than an OBO Parser. Always check your results!!

Some of the scripts are self-documenting, run with "-h" on the command
line. The documentation is probably incomplete, it's often better to
just look at the script, they're brain-dead enough to figure out
what's going on.

caveat emptor!

For a proper perl obo parser, see:

* http://search.cpan.org/~cmungall/go-perl/

And its replacement:

* http://search.cpan.org/~cmungall/GOBO/