[Biopython-dev] [Biopython] AlignACE Application Wrapper

Christian Brueffer christian at brueffer.de
Thu Nov 29 11:06:01 UTC 2012

On 11/29/2012 06:56 PM, Peter Cock wrote:
> 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.

(moved to biopython-dev)

Indeed.  I already have a cleaned up wrapper and unit tests in my local 
tree, but I don't want to submit them without actually testing them with 
an up to date binary ;-)

archive.org has a version of http://atlas.med.harvard.edu/ from 2011,
I have contacted the responsible person mentioned on the page.



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