[Biopython-dev] SeqIO

Thomas Sicheritz-Ponten thomas at cbs.dtu.dk
Fri Sep 28 00:51:45 EDT 2001

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.


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

	De Chelonian Mobile ... The Turtle Moves ...

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