[Biopython-dev] SeqRecord to file format as string

[Jared Flatow]

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 others.

However, py3k and 2.6 will make available the functionality described  
in PEP 3101:

http://www.python.org/dev/peps/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.

Best,
jared