[Biopython] Could Bio.SeqIO write EMBL file?

Peter biopython at maubp.freeserve.co.uk
Thu Jan 7 18:14:20 UTC 2010


On Thu, Jan 7, 2010 at 4:08 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
>
> Great. I've just committed very basic EMBL output support to our main
> branch on git. This is a stepping stone, deliberately a partial solution only
> for now, to make sure the basics seem to work (dealing with the sequence
> and identifiers, but nothing about the detailed annotation). In particular,
> I have deliberately not implemented feature support (yet - the existing
> code for writing a GenBank feature table will need to be tweaked to
> cover EMBL feature tables as well).
>
> I realise that in the current state this isn't going to be especially useful
> for you, but if you can have a look anyway and let me know if there is
> anything amiss that would be helpful. e.g. Make sure your favourite
> tools like the EMBL files Biopython produces. What do you use?
> Artemis?

I did some more work, including writing CO lines for CONTIG records,
but when testing realised our EMBL parser doesn't (yet) cope with them:
http://bugzilla.open-bio.org/show_bug.cgi?id=2980

Peter



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