[Biopython-dev] SeqRecord to file format as string
jflatow at northwestern.edu
Wed Jun 18 15:25:18 UTC 2008
On Jun 18, 2008, at 10:16 AM, Jared Flatow wrote:
> Hi Peter,
> On Jun 18, 2008, at 9:00 AM, Peter wrote:
>> Jared - On reflection, do you think adding a method like this to the
>> SeqRecord (or even just for the FASTA format) would be useful?
> Yes I still think so. In fact, for sequences, I would say that I
> pretty much never deal with a format ever than FASTA, so even making
> the __str__ method of SeqRecord return the FASTA format as well
> seems reasonable, though perhaps my use cases are different than
> However, py3k and 2.6 will make available the functionality
> described in PEP 3101:
> I think it would be best to define some semantics that are
> compatible with this PEP. This would basically mean using the
> __format__ method (which could be the same as the tostring method
> you have defined below). To achieve backward compatibility and/or a
> more OO interface, tostring could just be an alias for __format__.
> Thus, instead of calling format(seq_rec, 'fasta') one could call
> seq_rec.tostring('fasta') and these would be equivalent. The PEP
> also states that format(seq_rec) should be the same as str(seq_rec).
On second thought it seems like a .format method (similar to the one
the string class is acquiring) should be used as an alias to
__format__ (somehow I think tostring should always be the same as
> In short, I think creating methods to return formatted versions of
> objects (SeqRecords) is a good idea, but most especially if it is
> done in a way consistent with the language's vision.
More information about the Biopython-dev