[Bioperl-l] problem setting -find option for EMBOSS getorf
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
USA web: http://www.scitegic.com
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