[Biopython-dev] MAF Parser/Indexer

Peter Cock p.j.a.cock at googlemail.com
Mon Apr 2 08:26:16 UTC 2012

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 :)

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.


More information about the Biopython-dev mailing list