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

Scott Markel smarkel at scitegic.com
Thu Aug 19 21:28:38 EDT 2004

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 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
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