[Biopython-dev] [Bug 2680] Bio.AlignAce.Parser.py need to import string

[Bruce Southey]

Peter wrote:
> On Fri, Nov 21, 2008 at 3:32 PM, Bartek Wilczynski
> <bartek at rezolwenta.eu.org> wrote:
>   
>> Hello,
>>
>> I fixed the bug (changed both uses of string.atof() to float() ), and
>> commited to CVS, although I cannot close it in Bugzilla (my
>> dev.open-bio account does not seem to work for bugzilla).
>>
>> cheers
>> Bartek Wilczynski
>>     
>
> Thanks Bartek,
>
> I was partway through the build process for the Biopython 1.49
> release, but I've got that latest Bio/AliceAce/Parser.py file now.
> I've closed Bug 2680 - I'm not sure how the permissions work on
> Bugzilla exactly...
>
> On a related note - could you write a unit test for Bio.AlignAce please?
>
> Thanks,
>
> Peter
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>
>   
Hi Bartek,
I just started on working through understanding the functionality of the 
code so it would be really great to the tests and a tutorial section on 
AlignAce.

So far I know that there needs to be at least two tests for AlignAce:
1) Running  Bio.AlignAce.AlignAceStandalone
2) Parsing the output  from AlignAce

There needs to be similar tests for CompareAce.

Also, could you please add the following lines to your AlignAce2004 code 
(I downloaded it from your site yesterday) to standard.h?

#include <limits.h>
#include <string.h>

I needed these to compile AlignAce under Linux with gcc version 4.3.2. I 
would also suggest not to include binaries because they are statically 
linked to old C++ libraries. Running just './AlignACE' gives the error:
./AlignACE: error while loading shared libraries: libstdc++.so.5: cannot 
open shared object file: No such file or directory

Thanks
Bruce