[Biopython-dev] MAF Parser/Indexer

[Peter Cock]

On Sun, Apr 1, 2012 at 9:30 PM, Brad Chapman <chapmanb at 50mail.com> wrote:
>
> Andrew;
> Thanks for putting this together. It looks great, is well integrated
> with AlignIO and it's awesome to see a test suite.

Indeed, +1 on tests :)

Apologies for not replying earlier - this was flagged in my email
client all of last week.

> I dug through the code and my small suggestions would be:
>
> - Could you refactor some of the larger functions into separate smaller
>  components? A couple of these spread over a ton of lines and it can be
>  a bit difficult to follow the logic throughout:
>
> ...
>
>  As a practical example, here you have a large block which checks the
>  SQLite index matches the MAF file and everything looks okay:

Maybe I should do the same with the SeqIO SQLite code.

> - Would you be able to put together a small example for the
>  Cookbook or Tutorial documentation? This would be a great way to help
>  others get started with the functionality and advertise it.

He already has - very organised :)
http://biopython.org/wiki/Multiple_Alignment_Format

Is there any more about reverse complemented sequences
and how they are handled, for in simple iterators, but more
so when indexing? What I'm getting at here is the non-typical
treatment of start and end being relative to the reverse
complemented sequence for minus strand alignments. Here
most tools/formats always count from the first base on the
forward strand.

Peter