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

[Jason Stajich]

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.


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

---------- Forwarded message ----------
Date: Thu, 17 Jan 2002 08:04:39 -0500
From: bioperl-bugs@bioperl.org
To: bioperl-guts-l@bioperl.org
Subject: [Bioperl-guts-l] Notification: incoming/1066

JitterBug notification

new message incoming/1066

Message summary for PR#1066
	From: cann0010@tc.umn.edu
	Subject: Request ID regex not matching Blast "wait" page
	Date: Thu, 17 Jan 2002 08:04:38 -0500
	0 replies 	0 followups

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Date: Thu, 17 Jan 2002 08:04:38 -0500
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From: cann0010@tc.umn.edu
To: bioperl-bugs@bioperl.org
Subject: Request ID regex not matching Blast "wait" page

Full_Name: Steve Cannon
Module: retrieve_blast.pl
Version: 0.9.0
PerlVer: 5.6.0
OS: OS X 10.1.2
Submission from: ecannon.dsl.visi.com (208.42.18.252)


The retrieve_blast.pl script in the 0.9.0 distribution doesn't work for me (I
don't remember the error message) without making the following change to the
module. I suspect the Blast "wait" page has changed the format of its request
ID. I changed the first line below to the second:

	if($data =~ /RID" VALUE="(\S+)"/s) {
	if($data =~ /RID = (\d+-\d+-\d+)/s) {


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