[Bioperl-l] Bio::Tools::Run::RemoteBlast return codes

Scott Markel SMarkel at accelrys.com
Thu Jan 14 17:58:06 EST 2010

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

Vice President, Board of Directors:
    International Society for Computational Biology
Chair: ISCB Publications Committee
Associate Editor: PLoS Computational Biology
Editorial Board: Briefings in Bioinformatics

More information about the Bioperl-l mailing list