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Question about map2slim

Chris Mungall cjm at fruitfly.org
Fri Jan 28 16:52:50 PST 2005


Andy,

The reason you are seeing repeated lines is because you are using the -t
option, to format the results as a tree. If there are multiple paths from
a term to the root term then the term will be written multiple times, just
like in the AmiGO display.

Hope that helps
Chris

On Fri, 21 Jan 2005, Andrew Nunberg wrote:

> 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
>


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