[Biopython] Could Bio.SeqIO write EMBL file?

[Peter]

On Thu, Mar 4, 2010 at 2:26 PM, Anne Pajon <ap12 at sanger.ac.uk> wrote:
> Hi Peter,
>
> I'm happy to work with git. I've already read the bioython wiki page on it
> so I'm hoping to do the right thing.

OK - now you get to try doing a merge (grin), as I have committed the
SQ line change (with some minor changes, for example I changed your
variable names to keep the line length down).

> I'm going to commit and push the ID line fix as soon as I am happy with it,
> and to see if I understood how it should be done. Looking forward to get
> your feedback.

One minor issue is you accidentally checked in the BioSQL database
created by the unit tests. I've update the .gitignore file to stop this
happening to someone else.

The EMBL data division stuff makes sense (I simply hadn't gotten
round to it when I was doing it for the GenBank output).

Some of your other changes need to be co-ordinated with the EMBL
(and GenBank) parser. See also Bug 2578,
http://bugzilla.open-bio.org/show_bug.cgi?id=2578

In the case of PR (project lines) I think we must be ignoring them at
the moment, but to match the GenBank parser the information should
be stored in the SeqRecord dbxrefs list not the annotations dictionary.

Regards,

Peter