[Bioperl-l] Fwd: BioPerl and BioLib

Chris Fields cjfields at illinois.edu
Fri Feb 6 09:55:53 EST 2009


swig does handle C++ templates but they are definitely trickier to  
work around.  I have tried a little XS-based wrapping of seqan and it  
is definitely not for the faint of heart (I gave it up, just not  
enough tuits).

chris

On Feb 6, 2009, at 7:50 AM, Chad Davis wrote:

> If you're looking for requests, how about something for structural
> bioinformatics:
>
> http://www.bioinf.uni-sb.de/OK/BALL/
>
> ... though BALL might be as difficult as SeqAn, as it's also C++/ 
> templated.
> Though, I believe it already provides Python bindings (via Swig?).  
> Maybe
> that makes it easier ...
>
> Chad
>
> On Fri, Feb 6, 2009 at 14:02, Chris Fields <cjfields at illinois.edu>  
> wrote:
>
>> I'll forward this onto the list.  Something that links into EMBOSS  
>> would be
>> nice, or even SeqAn.  SeqAn may be a bit of challenge as it is C++  
>> and uses
>> templates:
>>
>> http://www.seqan.de/
>>
>> BTW, the NCBI toolset has a perl API but there are several problems  
>> with it
>> not least being it's precompiled only for Linux:
>>
>> ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools%2B%2B/2008/Mar_17_2008/ 
>> Perl/
>>
>> -c
>>
>> Begin forwarded message:
>>
>> From: Pjotr Prins <pjotr2009 at thebird.nl>
>>> Date: February 6, 2009 3:38:42 AM CST
>>> To: Chris Fields <cjfields at illinois.edu>
>>> Subject: BioPerl
>>>
>>> Hi Chris,
>>>
>>> While we are at it, and in the flow, I would like to add another
>>> library to biolib. What do you suggest is a need for? Maybe you can
>>> post a question on the BioPerl mailing list? Anything that will give
>>> some real users. Emboss Nucleus or AJAX? Or some part of the NCBI
>>> toolset?
>>>
>>> Pj.
>>>
>>
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