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

[Michiel de Hoon]

Peter wrote:
>> 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.

In my opinion, the new Bio.SeqIO code is a huge improvement to 
Biopython, so I'd be happy to make a new release for it.

As far as I know, with the recent patches there are no major issues with 
the Blast XML parser in CVS (correct me if I'm wrong).

For Bio.SeqIO, we're also in pretty good shape, as far as I can tell. 
 From what I remember, the remaining issues were
1) Which functionality to include, in particular
   a) if functions should accept file names in addition to file handles;
   b) if functions should infer the file format from the file extension, 
the file content, or otherwise.
2) What are the best names for the functions that the user will see.

For the next Biopython release (code-named "Bronx"), one solution would 
be to exclude any functionality for which we're not sure if it's really 
desirable (but keep it in CVS for the next round). This is essentially 
the functions in Bio/SeqIO/__init__.py. Then, we'll only need to 
converge regarding 2) to be ready for a new Biopython release.

--Michiel.