[Bioperl-l] EMBOSS/water interface

[Mike Muratet]

On Thu, 3 Feb 2005, Mike Muratet wrote:

> 
> 
> 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
> 
> 
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> 
Jason

I think I spoke too soon. You can pass an array, you just need to call it
bsequence.

thanks

Mike