[Bioperl-l] Bio::SeqIO::kegg

[Hilmar Lapp]

t/SeqIO......................ok 48/230"my" variable $annotation masks 
earlier declaration in same scope at blib/lib/Bio/SeqIO/kegg.pm line 
202, <GEN13> line 235

	-hilmar

On Monday, October 20, 2003, at 06:46  PM, Allen Day wrote:

> Hi all,
>
> I just added a parser for KEGG sequence records, available from:
>
> ftp://ftp.genome.ad.jp/pub/kegg/genomes/genes/
>
> I've parsed all tags except CODON_USAGE and POSITION into a
> Bio::Seq::RichSeq.  I didn't implement CODON_USAGE because I wasn't 
> sure
> what class would hold it, and also because the codon frequencies can be
> recalculated from the primary sequence.
>
> For the POSITION tag, I didn't implement it because I wasn't sure how 
> to
> deal with the reference sequence and exon positions for a spliced mRNA.
> If someone wants to explain to me how to do this, I'd be happy to
> implement it.  Or if someone wants to DIY, please feel free.
>
> I'm in the process of writing a parser for KGML:
>
> ftp://ftp.genome.ad.jp/pub/kegg/pathways/KGML_v0.3/
>
> to read in KEGG's pathway data, are people interested in representing
> metabolic networks in bioperl, or am I better off doing this as a 
> separate
> project?  Or better yet, has someone already done this?
>
> -Allen
>
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>
-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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