[Bioperl-l] Bio::Factory::EMBOSS synopsis

Bernd Web bernd.web at gmail.com
Fri Sep 15 04:50:00 EDT 2006


Hi Brian,

I used 2.9.0 and 4.0.0.
Below I include the adapted synopsis. This example works untill the
alignment handling. The water alignment output also changed, so no
alignment are parsed (no problem for me, i do not use this).

The synopsis is on:
http://doc.bioperl.org/releases/bioperl-current/bioperl-run/Bio/Factory/EMBOSS.html
and:

http://doc.bioperl.org/releases/bioperl-current/bioperl-run/Bio/Tools/Run/EMBOSSApplication.html


On the first, there is a small error in Description: set
"$factory->verbose"  should be set "$prog->verbose".


Bernd

- Hide quoted text -

On 9/15/06, Brian Osborne <osborne1 at optonline.net> wrote:
> Scott and Bernd,
>
> The names of the parameters passed to EMBOSS applications have changed over
> the past EMBOSS versions, Bioperl handles older versions. Some discussion:
>
> http://article.gmane.org/gmane.comp.lang.perl.bio.general/7682/match=emboss
>
> Bernd, what version EMBOSS are you using?
>
> Brian O.


More information about the Bioperl-l mailing list