[Bioperl-l] Re: [Bioperl-guts-l] Notification: incoming/1066 (fwd)

[Steven Cannon]

On Thursday, January 17, 2002, at 07:44 AM, Jason Stajich wrote:

> From: Jason Stajich <jason@cgt.mc.duke.edu>
> Date: Thu Jan 17, 2002  07:44:42 AM US/Central
> To: Bioperl <bioperl-l@bioperl.org>
> Cc: Steven B Cannon <cann0010@tc.umn.edu>
> Subject: [Bioperl-guts-l] Notification: incoming/1066 (fwd)
>
> retrieve_blast.pl is an older script - we should update it or consider
> pointing people to a newer module based system for remote blast -
> see the module Bio::Tools::Run::RemoteBlast.  This module provides the
> functionality of submitting and retrieving results from the NCBI blast
> queue.
>
> See the test
> t/RemoteBlast.t
>
> for a good example of how this works.  We need to add better SYNOPSIS
> and documentation to the module which is my fault.  It is in the works 
> for
> our 1.0 release.

Sounds good. By the way, where this error came up for me was via the 
0.9.0 bptutorial.pl, section III.4.2 (so it sounds like this should 
receive an edit):

"Consequently, it is recommended to use, and if necessary
modify, the supplied scripts - run_blast_remote.pl and
retrieve_blast.pl in the examples/blast/ subdirectory - rather than to
use Blast.pm directly.  Sample syntax looks like this:

    run_blast_remote.pl seq/yel009c.fasta -prog blastp -db swissprot
    retrieve_blast.pl < YEL009C.blastp2.swissprot.temp.html
"

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