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Question about map2slim
Andrew Nunberg
anunberg at oriongenomics.com
Fri Jan 21 09:54:26 PST 2005
I have tried to run map2lim to map a collection of proteins of interest to
the generic go slim to make a pie chart.
When running map2lim I get errors from parsing the ontology file, here is
an example
<error>
<message>missing namespace for ID: GO:0008291</message>
<file>gene_ontology.obo</file>
<parse_class>GO::Parsers::obo_text_parser</parse_class>
</error>
I used the c option to get a count, but I have noticed that some of the
slim terms are repeated
Eg.
GO:0016049 cell growth (cell growth) 4 4
biological_process
GO:0009790 embryonic development (embryonic development) 3 3
biologic
al_process
GO:0040007 growth (growth) 1 5 biological_process
GO:0016049 cell growth (cell growth) 4 4
biological_process
GO:0009653 morphogenesis (morphogenesis) 21 24
biological_process
GO:0016049 cell growth (cell growth) 4 4
biological_process
Am I doing something wrong?
Andy
--
Andrew Nunberg
Bioinformagician
Orion Genomics
(314)-615-6989
www.oriongenomics.com
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