[Biopython-dev] MAF Parser/Writer/Indexer

[Peter Cock]

On Mon, May 16, 2011 at 12:14 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>
> I started work on merging the basic parser/writer into Biopython
> on this new branch,
>
> https://github.com/peterjc/biopython/tree/alignio-maf
>
> As I think I mentioned by email before, there were some PEP8
> formatting changes (removing spaces before brackets).
>
> ...
>
> Note that right now, test_AlignIO.py is still not passing (which
> is a major reason why I haven't merged this to the trunk).
> Currently the issue is to do with how you are parsing species
> names, assuming database.chromosome is not possible in general.

I've changed it to preserve the identifier as is for the SeqRecord
id field, got all the test suite passing, and added a couple of small
MAF files from the BioPerl test suite (which highlighted some more
issues).

Do you think it makes sense to automatically promote any dots
(periods) in the sequence to the letter of that position in the first
sequence? This is something I'd been thinking we should do in
the PHYLIP parser as well. See the MAF/humor.maf example.

Peter