[Bioperl-l] problem setting mismatch penalty in StandAloneBlast.pm without setting quiet()

Scott Markel smarkel at scitegic.com
Mon Jul 19 16:47:26 EDT 2004

I'm using BioPerl 1.4 on a Windows XP box.  When I set the
mismatch penalty for blastn, I get both the "-q" command line
option, which I want, and errors getting redirected to /dev/null,
which I don't want.  The problem seems to be the following
line in Bio::Tools::Run::StandAloneBlast's _setparams():

   if ($self->quiet()) { $param_string .= '  2>/dev/null';}

A constructor call

   $factory = Bio::Tools::Run::StandAloneBlast->new(@params);

followed by either $factory->q(-3) or $factory->quiet(-3)
both result in "-q -3" being added to the command line *and*
"  2>/dev/null" being appended to the command line.

I've tried calling $factory->verbose() with verbosity values
of -1, 0, 1, and 2, but this didn't get rid of the /dev/null

How do I set the mismatch value without tripping $self->quiet()
in StandAloneBlast.pm?


Scott Markel, Ph.D.
Principal Bioinformatics Architect  email:  smarkel at scitegic.com
SciTegic Inc.                       mobile: +1 858 205 3653
9665 Chesapeake Drive, Suite 401    voice:  +1 858 279 8800, ext. 253
San Diego, CA 92123                 fax:    +1 858 279 8804
USA                                 web:    http://www.scitegic.com

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