[Biopython] AlignACE Application Wrapper

[Christian Brueffer]

On 11/29/2012 10:42 AM, Christian Brueffer wrote:
> 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).
>

Some of the test files in the Tests directory mention the following 
AlignACE version: "AlignACE 4.0 05/13/04"

This may be the answer to my problems.  Does anyone know where to get 
hold of this version?

The website (http://atlas.med.harvard.edu/) is down and the only
other one I found (http://arep.med.harvard.edu/mrnadata/mrnasoft.html)
only distributes the old 2.3 version that I have.

Cheers,

Chris