[Biopython-dev] Reading sequences: FormatIO, SeqIO, etc

[Albert Krewinkel]

Peter wrote:
> > Peter wrote:
> >>Oh - you meant just adding EMBL feature iteration.  I was thinking 
> >>about the larger task of full EMBL file reading.
> >
> Albert wrote:
> >I started working on that, but I'm not very far yet.
> 
> Are you starting from Bio.GenBank or from scratch?  I would point out 
> that the code in Bio.GenBank was inserted into what was once a Martel 
> based parser, and designed to be a transparent change for the end user.
>
> What I would like to do is recycle that code into a new far simpler 
> SeqIO GenBank parser which would only return SeqRecords.  In particular 
> I would get rid off all the scanner/consumer model with all its function 
> callbacks.
> 
> At this point I would try and handle both GenBank and EMBL files together.

I didn't do much more than to play with current code and add some
methods to parse EMBL specific things.  The results can be found here:

http://www.inb.uni-luebeck.de/~krewink/embl.py

It's ugly, and doesn't provide much functionality, but could be a
starting point.

Albert

-- 
Albert Krewinkel <krewink at inb.uni-luebeck.de>
University of Luebeck, Institute for Neuro- and Bioinformatics