[bip] Blog post on bioinformatics and Python

[Peter]

Titus Brown wrote:
>
> Why not:
>
>   data = list(data)
>
> ?  That will take any iterator/generator and turn it into a list.
> There's no real penalty for doing this (if you need a random access
> list, then you need to fully parse the file anyway!), and you can
> convert it into a dictionary pretty easily, too.

We this in the Biopython tutorial in the context of turning a SeqIO
sequence iterator into a list, but perhaps it warrants a mention in
the BLAST parsing section too.

> OTOH, frustration with the opaqueness of BioPython BLAST objects (and
> the use of crmpd 'sbjct' vrbl nms) led me to write my own blastparser
> with objecs that had a useful 'dir', were debuggable by me, had lots of
> automated tests, etc.  You could take a look at that, although it is
> sloooooooooooooooooooooow.
>
>        http://darcs.idyll.org/~t/projects/blastparser/
>        http://darcs.idyll.org/~t/projects/blastparser-latest.tar.gz
>

In order to maintain backwards compatibility, we are unfortunately
stuck with the compressed variable names now (although we could add
aliases).  Having a go at improving the explorablity of the BLAST
object structure at the python prompt is a fairly specific and
concrete target.  Making the __str__ and __repr__ methods here more
helpful is something I'd been meaning to have a go at.

The Biopython BLAST parsers already have plenty of tests - but I'm
sure there is room for more.  What license is your code under, and in
particular could we use any of your test files in Biopython?

Peter