[Biopython-dev] Getting nucleotide sequence for GenBank features

[Peter]

On Tue, Nov 3, 2009 at 11:41 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
>
> Certainly there are good reasons for wanting to be able to take
> a SeqFeature and the parent sequence (SeqRecord or Seq)
> and create a SeqRecord (either plain nucleotides or translated
> into protein). e.g. pretty much all non-trivial GenBank to FASTA
> conversions. Offering this as a SeqRecord method might be the
> best approach, option (4).
>
> However, this is I think on top of the more fundamental step
> of just extracting the sequence (without worrying about the
> annotation). Here as noted above, I currently favour adding
> a method to the SeqFeature, option (1). How about as the
> method name get_sequence, extract_sequence or maybe
> just extract?

Done on a github branch, comments welcome:
http://github.com/peterjc/biopython/tree/seqfeature-extract

If that seems the best way to expose this functionality
(i.e. option (1) from my earlier list of suggestions), I can
commit this to the trunk, and we can move on to the
related idea of how to this nicely with get SeqRecord
objects for SeqFeatures.

Peter