[BioPython] what to use for working with fasta sequences and alignments?

[Jan Kosinski]

Hi,

Indeed, the answer was already on the webpage you have pointed, I should 
have read it more carefully.

I will start to be brave ;-) and use the current biopython from your CVS.

Can you estimate already when you going to release new SeqIO (this year?)?

Janek

Peter wrote:
> Jan Kosinski wrote:
>> Are you going to fix this in the new SeqIO?:
>>
>> When using Bio.SeqIO.FASTA.FastaReader the names of the sequences are 
>> stripped away after the first "space".
>>
>> Janek
>
> The code in Bio.SeqIO.FASTA is some of the old undocumented stuff, and 
> I don't think we should change it in case anyone is depending on the 
> old behaviour.  Its not part of the "new" Bio.SeqIO code I've been 
> working on described here:
>
> http://biopython.org/wiki/SeqIO
>
> My plan is that once the new Bio.SeqIO code is considered stable, to 
> make Bio.SeqIO.FASTA as depreciated.
>
> If you really want to use Bio.SeqIO.FASTA, look at the 
> record.description field for the rest of the name.
>
> Peter