[Bioperl-l] DB::GenBank/DB::GenPept and SearchIO::fasta

[Jason Eric Stajich]

I've updated the pointer to the NCBI cgi script for web based seq
retrieval.  One casualty is that Batch Retrieval doesn't seem to be
working - I haven't been able to play with the CGI parameters enough to
see what is the appropriate syntax to specify multiple retrieval ids in
the 'term' box- the 'query' cgi only supports GET requests and it isn't
totally apparent what the batchentrez.cgi parameters are beyond
cmd=Retrieve and db=n.  Something to play with at some point.

The DB.t tests have been updated to ignore problems with Batch retrieval
for the time being.

This fix also addressed Brian Osborne's bug #1041 about not being able to
retrieve PIR or SwissProt seqs from GenPept with a gi number.


I've also commited Bio::SearchIO::fasta for parsing FASTA reports this
afternoon which has only been tested on FASTA DNA vs DNA and Protein vs
Protein reports.

Enjoy.
Jason

-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu