[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 18:44:09 UTC 2009


biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
Attachment #1296 is|0                           |1
           obsolete|                            |

------- Comment #33 from biopython-bugzilla at maubp.freeserve.co.uk  2009-05-12 14:44 EST -------
(From update of attachment 1296)
(In reply to comment #32)
> Added PROBCONS and TCOFFEE command line interfaces and unittests.
> The TCOFFEE commadline implements a very restricted set of options
> (just those Brad attached). 
> Also added white list of known headers to AlignIO/ClustalwIO.py:97 - the
> PROBSCONS unittest will fail without this alteration.
> On http://github.com/cymon/biopython-github-master/tree/applic-int

Thank you Cymon and Brad - those are now checked in, more or less as is.
I did tweak Bio/AlignIO/ClustalwIO.py a little bit.  Also, TCoffee says it can
be installed on Windows using Cygwin - we should try that at some point ;)

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.

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)?


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