[Biopython] missing fields in SeqIO EMBL parser?

Peter biopython at maubp.freeserve.co.uk
Fri May 7 13:23:56 UTC 2010


On Fri, May 7, 2010 at 2:04 PM, Wim De Smet <Wim.DeSmet at ugent.be> wrote:
> Hi,
>
> I'm trying to parse an embl file using Bio.SeqIO but I'm missing some
> metadata fields in the parsed object. For one, I can't find any reference to
> the DT (date) fields or any of the database cross references. I'm using
> biopython 1.53.
>
> Is this simply not implemented yet or are there options to include this data
> in the SeqRecord object returned?

The DT lines are currently ignored, please file an enhancement bug.
This is complicated by the fact the GenBank files have only one date,
and the EMBL parser shares a lot of code with the GenBank parser.

Could you be a bit more precise about missing database cross references?
i.e. What line type are you looking for?

Thanks.

Peter



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