[Bioperl-l] need help

Chris Fields cjfields at uiuc.edu
Fri Aug 31 10:51:51 EDT 2007


I don't believe Bio::SeqIO::kegg will parse those files (they aren't  
sequence files).  The format it recognizes is:

http://www.bioperl.org/wiki/KEGG_sequence_format

for the files found in the subdirectories here:

ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms

I would just build a custom parser if all you're interested in is id/ 
names/synonyms.  It'll be much faster.

chris

On Aug 31, 2007, at 4:41 AM, neeti somaiya wrote:

> Hi,
>
> I am trying to parse the compound (
> ftp://ftp.genome.jp/pub/kegg/ligand/compound/compound) and glycan (
> ftp://ftp.genome.jp/pub/kegg/ligand/glycan/glycan) files of KEGG using
> bioperl.
> I just want the kegg id of the compound/glycan and its names and  
> synonyms if
> any.
> Bio::SeqIO is giving some problem, I am not able to fetch the id  
> and name.
> Can someone help me with this.
>
> Thanks.
>
> -- 
> -Neeti
> Even my blood says, B positive
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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