[Biopython-dev] [Bug 2815] Bio.Application command line interfaces

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Tue May 12 19:45:12 UTC 2009


------- Comment #34 from cymon.cox at gmail.com  2009-05-12 15:45 EST -------
(In reply to comment #33)
> Note for the TCoffee suite we could also consider adding xpresso, 3dcoffee,
> mcoffee and rcoffee as well - hopefully they have similar interfaces so with
> some subclassing we won't have to duplicate a lot of the code.

With the latest version of t_coffee (and not the currently available Jaunty
package!), these (ie the meta calls like mcoffee etc) are all covered by the
"-mode" option. I just installed t_coffee from source and this appears to be
the case. There are so many options and interdependencies in TCOFFEE, and its
command line is clearly a moving target, that the interface may require more
work before being released.

> One other thought - do you think the EMBOSS water and needle wrappers (and any
> other alignment tools in EMBOSS) be made available under Bio.Align.Applications
> (via an import in Bio/Align/Applications/__init__.py so no code duplication)?

Sounds good to me.

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