[Biopython-dev] Accessing ExPASy through Bio.SwissProt / Bio.SeqIO

[Michiel De Hoon]

> Or do we want to encourage Bio.SeqIO (which happens to call
> Bio.SwissProt.SProt internally)?
> 
> >>> from Bio SeqIO
> >>> from Bio import ExPASy
> >>> handle = ExPASy.get_sprot_raw("O12345")
> >>> record = SeqIO.parse(handle, "swiss")
> 
> This is the style I prefer (and is very similar to the related
> examples I added to the tutorial).  It separates fetching the data (as
> a handle) and parsing it (via SeqIO).

SeqIO.parse returns a SeqRecord; a SwissProt.parse returns a
SwissProt.SProt.Record.
Does the SeqRecord contain the same information as a SwissProt.SProt.Record?
Or is some information lost?
If they contain the same information, then I am in favor of encouraging
Bio.SeqIO.

--Michiel.


Michiel de Hoon
Center for Computational Biology and Bioinformatics
Columbia University
1150 St Nicholas Avenue
New York, NY 10032