[Biopython] EMBL DNA records with locations referencing other sequences

Peter Cock p.j.a.cock at googlemail.com
Fri Oct 4 16:12:46 UTC 2019


That's more or less exactly what I had in mind. Do you have this on a
branch of a public git repository?

One tweak I was considering is accepting a dictionary-like object where
the values could be SeqRecord rather than Seq-like objects. The reason
being that those are easy to get via Bio.SeqIO.index(...) or
Bio.SeqIO.index_db(...), and should be perfect for when you have already
downloaded the referenced accessions (e.g. a folder of GenBank files).

Peter

On Fri, Oct 4, 2019 at 4:34 PM Adam Sjøgren <asjo at koldfront.dk> wrote:
>
> Adam writes:
>
> > If the location refers to other records, those records can be supplied
> > in an optional references dictionary, where the records will be looked
> > up by the ref (key) and the value is expected to be the same as the
>>                                                              type
> > parent_sequence parameter.
>
>
> --
>  "You make a hit by putting two flops together"               Adam Sjøgren
>                                                          asjo at koldfront.dk
>
> _______________________________________________
> Biopython mailing list  -  Biopython at mailman.open-bio.org
> https://mailman.open-bio.org/mailman/listinfo/biopython



More information about the Biopython mailing list