[Biopython-dev] SeqIO

[Thomas Sicheritz-Ponten]

Brad Chapman <chapmanb at arches.uga.edu> writes:

thx for the comments !

> One big question I have is, how many of the features do you want to
> try and retain in the conversion? So, for GenBank format, do you
> want me to just write out the basic information (sequence, type,
> etc) and ignore the feature table, or do we want to somehow map the
> features from format to format (ie. EMBL <-> GenBank).
All of them. I think each GenBank feature has an exact equivalence in EMBL
and SwissProt (GenPept). So that leaves us just with the definition of the
corresponding feature names.

> 
> If we want to think about feature conversion, this'll be tougher and
> we'll need to think about converters between "similar" formats like
> EMBL and GenBank.
GenBank, EMBL and SwissProt ... where EMBL and SwissProt are almost
identical (I think...)

> => Why are you duplicating SeqRecord in the SeqIO stuff instead of
> just reusing it? I don't think I understand what you are talking
> about with stripping newlines...
I copied everything so that I cóuld play around without breaking e.g. your
code. Now I think the changes are actually backward compatible - so we
could move it back.
> 
> => Is there a way to plug in a specialized converter for similar
> formats, like I was talking about above with EMBL/GenBank? I think
> Jeff suggested this earlier, and it seems like a good idea to me. I
> guess right now you could subclass ReadSeq and define your own
> Convert function, but maybe there is another way to do it.
I don't know if I understood this question...


A colleague and I, are thinking about converting SWISSPROT into a SQL
database for local use ...  which actually gets close to a former
discussion where Andrew and I dreamed about a python variant of SRS !  
My question: does anybody know about an already existing SQL tables for
SWISSPROT ? The step after that is actually creating an python interface for
generic queries, which would beat SRS ... at least on SWISSPROT.


cheers
-thomas

P.S. is anybody going to the Atlanta meeting in November ?
-- 
Sicheritz-Ponten Thomas, Ph.D  CBS, Department of Biotechnology
thomas at biopython.org           The Technical University of Denmark
CBS:  +45 45 252489            Building 208, DK-2800 Lyngby
Fax   +45 45 931585            http://www.cbs.dtu.dk/thomas

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