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

[Peter]

Jan Kosinski wrote:
> Hi,
> 
> Indeed, the answer was already on the webpage you have pointed, I should 
> have read it more carefully.

Don't blame yourself - you raised a good point, so I updated the Wiki to 
mention that old code.

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

Excellent - feed back is welcome.  Please have a look at the developer's 
mailing list archive if you are interested.

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

I am hopeful that we do the next of BioPython in the next few months - 
certainly this year.  However, no promises, as this is Michiel's 
decision, not mine.

In my opinion we need to finish sorting out the Blast XML support first. 
We have fixed a lot of issues in that area since BioPython 1.42 was 
released last year (the NCBI likes to tweak their file formats!).

When we make the next release, I would expect the new Bio.SeqIO code to 
be included but I would want to warn people that it is new "beta" code 
in the release notes.

Peter