Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with HTTPS or Subversion.

Download ZIP
standalone perl scripts for hacking obo files
Perl
branch: master

This branch is 9 commits behind cmungall:master

Fetching latest commit…

Cannot retrieve the latest commit at this time

Failed to load latest commit information.
GOBO
bin
t
templates
README
biomart-fetch.pl
gaf-grep.pl
gaf2gpx.pl
generate-daily-files.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-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-multi-merge.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-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

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/

Something went wrong with that request. Please try again.