[Bioperl-l] EMBOSS/water interface

Jason Stajich jason.stajich at duke.edu
Thu Feb 3 12:02:50 EST 2005

Jason Stajich
jason.stajich at duke.edu
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
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