[Bioperl-guts-l] [Bug 2317] New: Changing parameter MATRIX_NAME in RemoteBlast generates an error

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Tue Jun 12 10:48:55 EDT 2007


http://bugzilla.open-bio.org/show_bug.cgi?id=2317

           Summary: Changing parameter MATRIX_NAME in RemoteBlast generates
                    an error
           Product: BioPerl
           Version: 1.5 branch
          Platform: Macintosh
        OS/Version: MacOS X
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Unclassified
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: wollenbergk at mail.nih.gov


I'm running a script using Bio::Tools::Run::RemoteBlast, and when I include the
line of code:

  $Bio::Tools::Run::RemoteBlast::HEADER{'MATRIX_NAME'} = 'BLOSUM45';

the script generates two WARNINGs and doesn't write results to the output file.
The warnings are:

-------------------- WARNING ---------------------
MSG: req was POST http://www.ncbi.nlm.nih.gov/blast/Blast.cgi
User-Agent: bioperl-Bio_Tools_Run_RemoteBlast/1.5
Content-Length: 623
Content-Type: application/x-www-form-urlencoded

and

-------------------- WARNING ---------------------
MSG: <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" ...(a page
full of html)

When I comment out this line the script runs fine (reasonable BLAST output is
written to the output file). I get this error no matter which substitution
matrix I use, and BLOSUM45 is one of the available options for NCBI blastp. I
am running BioPerl 1.5.2 under Perl 5.8.6 on a Powermac G5 running OS 10.4.9.


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