[Biopython] AlignACE Application Wrapper

[Peter Cock]

Can we continue this on the biopython-dev mailing list (CC'd)?

On Thu, Nov 29, 2012 at 5:56 AM, Christian Brueffer
<christian at brueffer.de> wrote:
> 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 ...
>>
>> 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.

Hmm, I don't see any existing unit tests dedicated to this wrapper.
There should really be a file named test_AlignACE_tool.py or similar.

I would also like some doctests in Bio/Motif/Applications/_AlignAce.py
which must be non-executing so they can be run without dependencies,
which of course isn't actually a functional test but it does still catch some
issues - but primarily would be as documentation to demonstrate typical
usage.

I don't appear to have AlignAce installed on my own machines - in
particular, the nightly buildslaves don't have it. I don't think there is
a Debian/Ubuntu package for AlignAce, so testing this under
TravisCI is non-trivial - it looks like their licence agreement could
block packaging it.

Thanks,

Peter