[Bioperl-l] Bio::Tools::Run::RemoteBlast return codes
Scott Markel
SMarkel at accelrys.com
Fri Jan 15 15:40:31 UTC 2010
Chris,
It was nice meeting you and Scott C., too. And seeing Jason again.
If you and Mark
> How about returning 1, 2, 4 for the non-zero cases, with some
> error constants set for convenience? MAJ
are okay with adding more return values, that works best for us in
Pipeline Pilot.
I'll add a Bugzilla entry.
Scott
-----Original Message-----
From: Chris Fields [mailto:cjfields at illinois.edu]
Sent: Thursday, 14 January 2010 10:34 PM
To: Scott Markel
Cc: Bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] Bio::Tools::Run::RemoteBlast return codes
Scott,
I think this is fine (to change the third condition and retry with a specific code). The other possibility is to simply throw different exceptions under each of these circumstances, which can be caught via eval to allow a retry under only certain conditions (no content, for instance).
One interesting bit: I think (though I'm not sure) the new BLAST+ allows remote BLAST queries from command line, similar to the legacy blastcl3. Mark just wrote up a BLAST+ wrapper, so it might be worth testing that theory out.
chris
PS - BTW, nice to finally meet you at GMOD!
On Jan 14, 2010, at 4:58 PM, Scott Markel wrote:
> 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
>
> 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
>
> http://www.linkedin.com/in/smarkel
> Vice President, Board of Directors:
> International Society for Computational Biology
> Chair: ISCB Publications Committee
> Associate Editor: PLoS Computational Biology
> Editorial Board: Briefings in Bioinformatics
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
More information about the Bioperl-l
mailing list