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

[Jason Stajich]

I seem to think we already fixed this post 1.4 for you -- are you using
code from bioperl-run which is the most recent from CVS?
I don't seem to have a problem.

$ perl test_getorf.pl
Command line: getorf  -sequence /tmp/9ZnCEdDyL3/gid4fZXSrb -find 0 -auto

code:
 my $app = $f->program('getorf');
 $app->run({'-find' => 0,
	   '-sequence' => $seq});



-jason


On Thu, 19 Aug 2004, Scott Markel wrote:

> 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
>
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu