[Biopython-dev] powerful Alignment class in Biopython?

Jan Kosinski kosa at genesilico.pl
Thu Jan 11 11:34:50 UTC 2007


I have a feeling that it would be better to write all methods similar to 
BioPerl ones directly for BioPython Alignment class. The main reason is 
that this class is not related to any format like Fasta, Clustal or 
Nexus. It stores SeqRecords which are also not in Fasta or other format. 
It would make many things easier. For instance, I can write all my 
functions which do sth with alignments so that they accept general 
Alignment objects (and not necessarily FastaAlignment or 
ClustalAlignment objects ). Would not it better to write all stuff which 
do general things with alignments (column counting, column 
selection/removal etc.) so that it works with general Alignment class 
rather than with class for alignment of specific biological format?


Frank wrote:
> Hi Janek,
> then Nexus parser in Biopython (for which I still haven't written any
> documentation yet...) basically holds an alignment, and has some methods
> that deal with basic alignment functionality. If you're going to work on
> a more sophisticated alignment class, maybe we should try to get Nexus
> class and alignment class work smoothly together.
> Frank
> On Thu, 2007-01-11 at 09:52 +0100, Jan Kosinski wrote:
>> Hi,
>> Is anyone going to develop or developing now an Alignment class in
>> Biopython as powerful as for example SimpleAlign in Bioperl? Look here
>> for instance for methods available in Bioperl
>> http://doc.bioperl.org/releases/bioperl-1.2/Bio/SimpleAlign.html.
>> The reason I am asking is that I do not know if I should start working
>> on more functional subclass of biopython Alignment class (I do not want
>> to come back to Perl ;-)...
>> Regards,
>> Janek
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