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

[Allen Day]

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