[Biopython] AlignACE Application Wrapper

[Christian Brueffer]

Hi,

in preparation of cleaning up the AlignACE wrapper, I wanted to test
the current wrapper.   However, it doesn't seem to work at all and
the options do not match the ones that my AlignACE 2.3 binary provides
(which is surprising given that the binary is dated 1998 and the wrapper
copyright is much later).

I was wondering whether anyone uses the wrapper and I have a somehow
different AlignACE version.

For the record, here are the problems:

A simple test breaks immediately:

cline = AlignAceCommandline(input="f002")
stdout, stderr = cline()

Traceback (most recent call last):
   File "./test.py", line 5, in <module>
     cline = AlignAceCommandline(infile="f002")
   File 
"/home/chris/bin/python/lib/python2.7/site-packages/Bio/Motif/Applications/_AlignAce.py", 
line 38, in __init__
     "Input Sequence file in FASTA format."),
   File 
"/home/chris/bin/python/lib/python2.7/site-packages/Bio/Application/__init__.py", 
line 493, in __init__
     "%r for %s" % (description, names[-1])
AssertionError: ['input'] for input

This is not surprising, given the stray [input] lists in the parameter
list of all options in the wrapper.  These do not make sense with the
current application wrapper interface (maybe the interface changed at
one point?).

The following options are supported by the wrapper, but cannot be found
in the AlignACE help output: -minpass, -undersample, -oversample
-numcols appears, but it actually spelled -ncols

For the record, I'm testing with the Linux version of the binary
(AlignACE version 2.3  October 27, 1998).

Cheers,

Chris