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

[Michiel de Hoon]

Peter wrote:
> I would add a note saying doing it this way gives
> Bio.SwissProt.SProt.Record objects,
> while you could alternatively get SeqRecord objects as described in
> the SeqIO chapter
> (use a reference).

OK I will add that.
> 
> I'd suggested a Bio.SeqIO function, with a name like parse1() or
> parse_sole() etc which
> would return a single SeqRecord - and raise an error if the handle
> didn't contain one
> and only one record.  We could call this function read() if you prefer.
> 
I'd prefer read() instead of parse1(), parse_sole() etc. for the 
following reasons:

1) Having two names that are clearly different emphasizes the fact that 
they return different things (parse() returns an iterator, read() a record).

2) Some modules deal with data that always consist of one record (for 
example, gene expression data in case of Bio.Cluster). Such modules can 
have a read() function but not a parse(). It would feel strange if a 
module has a parse1() function but not a parse().

--Michiel.