[Bioperl-l] EMBOSS/water interface

[Mike Muratet]

On Thu, 3 Feb 2005, Jason Stajich wrote:

> 
> --
> Jason Stajich
> jason.stajich at duke.edu
> http://www.duke.edu/~jes12/
> On Feb 3, 2005, at 11:53 AM, Mike Muratet wrote:
> 
> > Greetings
> >
> > I'm trying to implement the Bio::Factory::EMBOSS to the 'water'
> > method (which coincidentally is the one used in the man page example). 
> > I'm
> > using EMBOSS 2.9.0 which is the latest on the emboss website. I get an
> > error 'Died: Unknown qualifier -seqall' which I interpret to mean the
> > emboss water method complaining that -seqall is not a valid argument. 
> > It
> > is, however, used in the man page. Furthermore, I don't see any
> > documentation for Bio::Factory::EMBOSS in the module documentation at
> > bioperl.org. Is this an obsolete method? Has anyone ever got the 
> > example
> > in the manpage to work?
> It is part of bioperl-run so check http://doc.bioperl.org/bioperl-run/
> 
> These problems reflect differences in EMBOSS-2.8.0 and EMBOSS-2.9.0 
> cmdline options.
> 
> If you do
> %water -help
> you'll see the names are now -asequence -bsequence
> 
> The tests in t/EMBOSS.t in bioperl-run have not been updated.  We'll 
> have to put some code in there which detects the version of EMBOSS and 
> updates the parameters appropriately.
> 
> 
> > Regards,
> >
> > Mike
> >

Jason

Thanks. I suspected as much. Too bad, the ability to pass an array was
cool.

Mike