[Biopython-dev] [Biopython (old issues only) - Bug #2815] (Closed) Bio.Application command line interfaces

[redmine at redmine.open-bio.org]

Issue #2815 has been updated by Markus Piotrowski.

Description updated
Status changed from New to Closed
% Done changed from 0 to 100

Commandline parser for MUSCLE has been merged to Biopython (ver. 1.5.1?)

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Bug #2815: Bio.Application command line interfaces
https://redmine.open-bio.org/issues/2815#change-15318

* Author: Cymon J.
* Status: Closed
* Priority: Normal
* Assignee: Biopython Dev Mailing List
* Category: Main Distribution
* Target version: Not Applicable
* URL: 
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Attached is a module to run the MUSCLE alignment programme based on the Bio.Applications interface.

A couple of helper functions are included MuscleAlign and ProfileMuscleAlign. Discussion on the dev-list suggests that helper functions are superfluous. Maybe, but I thought I'd include them anyway. A couple of unittests are included for the helper funcs.

C.

---Files--------------------------------
MuscleAlign.py (29.1 KB)
test_MuscleAlign.py (3.14 KB)
Applications.py (45.5 KB)
Applic.patch (1.45 KB)
TCoffeeCL.py (1.65 KB)


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