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GO slims

Ann Hedley ann.hedley at ed.ac.uk
Mon Mar 8 04:14:12 PST 2004


Hi

I have a postgres DB containing my protein identifiers and their 
associated GO accession numbers.  I want to get a high level summary of 
the proteins and I guess I need to use a goslim to do this but I can't 
find any clear instructions how to go about it.  Some of the problems 
I've got are...

I've downloaded, unzipped and expanded go_200402-assocdb-tables.tar.gz  
and a copy of My2Pg.pl but if I run the perl script in the 
go_200402-assocdb-tables dir it just hangs without any error messages. 

        $ My2Pg.pl
        ------------------------------------------------------------------
        -- My2Pg 1.28 translated dump
        --
        ------------------------------------------------------------------
         
        BEGIN;
 
 
then nothing.  I know it doesn't take any arguments so where should I be 
running it from?



I've read somewhere I could run map2slim on a remote db, and I've got 
this command

map2slim.pl -d go -o OUTPUTFILE SLIMFILE GENE-ASSOC-FILE

but what are (content and format) SLIMFILE and GENE-ASSOC-FILE?

Any help would be greatly appreciated.

Ann



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