[Bioperl-l] problem setting -find option for EMBOSS getorf

[Scott Markel]

I'm using BioPerl 1.4 on a Windows XP box, with EMBOSS version
2.7.1-Win-0.6.  I think my problem is with run() in
Bio::Tools::Run::EMBOSSApplication.  When I set the -find
option to 1 in the anonymous hash for $application->run()'s
argument list using

   "-find"       => $::findOptionID,

everything is fine, i.e., the command line looks like

   ... -find 1 -circular Yes ...

When the -find option is set to 0, the value never makes
it to the command line and I get

   ... -find -circular Yes ...

which clearly upsets getorf.

A quick work-around is to prepend a space to -find's value.

I checked the Open-Bio Bug Database and didn't find this
problem.  Anyone seen this before?

Scott

-- 
Scott Markel, Ph.D.
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