[Biopython-dev] SeqRecord to file format as string
jflatow at northwestern.edu
Wed Jun 18 15:16:59 UTC 2008
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 others.
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).
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.
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