[Bioperl-l] Bio::Tools::Run::RemoteBlast return codes
Mark A. Jensen
maj at fortinbras.us
Thu Jan 14 21:00:31 EST 2010
How about returning 1, 2, 4 for the non-zero cases, with some
error constants set for convenience? MAJ
----- Original Message -----
From: "Scott Markel" <SMarkel at accelrys.com>
To: <Bioperl-l at lists.open-bio.org>
Sent: Thursday, January 14, 2010 5:58 PM
Subject: [Bioperl-l] Bio::Tools::Run::RemoteBlast return codes
> We've been looking at Bio::Tools::Run::RemoteBlast after some feedback
> from our customers. Due to network irregularities (not sure what else
> to call it) users see the getting of remote BLAST results as somewhat
> random. When results come back the hits are fine, but sometimes no
> information comes back at all. Retrying helps.
> In looking at RemoteBlast.pm there are four "return -1" cases.
> * $status eq 'ERROR' (return on line 614)
> * $line =~ /ERROR/I (return on line 628)
> * !$got_content (return on line 648)
> * !$response->is_success (return on line 655)
> In the case of no content we'd like to retry remote BLAST. We're happy
> to do that part in our Pipeline Pilot Perl code wrapper for the BioPerl
> module, but we only want to retry in that case, not the other three.
> What would happen if that third "return -1" changed to a different
> return value?
> Scott Markel, Ph.D.
> Principal Bioinformatics Architect email: smarkel at accelrys.com
> Accelrys (Pipeline Pilot R&D) mobile: +1 858 205 3653
> 10188 Telesis Court, Suite 100 voice: +1 858 799 5603
> San Diego, CA 92121 fax: +1 858 799 5222
> USA web: http://www.accelrys.com
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