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

[Peter]

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