[Biophp-dev] Swissprot and Genbank parsers done

[Serge Gregorio]

>I just finished editing Serge's Genbank and Swissprot parsers to >work on our new approach.  They seem to be doing what they are >supposed to be doing.  

Btw, the ID field is set to the ENTRY NAME (right after LOCUS)
but should be the primary accession code.  That's one "bug"
that needs correcting.  Luckily, in most cases, their values
are the same.  =)  

>More rigurous testing would be nice.  Also, we might have to look 
>carefully at the structure of the output and do some work on >seq_factory to 'translate' the datastructures better.  

>Nevertheless, five sequence file formats down!  

Five?  What's the fifth?  Genbank, Swissprot, Fasta, PDraw, and...?
The Kegg Enzyme parser?  

>Shall we call the current Parse class: IOseq->read?  (and start >working on IOseq->write?)

Whatever you call the class, the "write" seems the next logical
thing to do.  I guess I'll write the "write" for Genbank and
Swissprot. 

Serge


Need a new email address that people can remember
Check out the new EudoraMail at
http://www.eudoramail.com