[Biopython] Could Bio.SeqIO write EMBL file?

[Anne Pajon]

Dear Peter,

Sorry for taking so much time to come back to you.

I've managed to fork the biopython repository on github and I think I  
am ready now to help writing improvements to Bio/SeqIO/InsdcIO.py by  
adding missing fields on the ID line and adding a PR line. I may look  
also at the SQ line.

Does this sound right to you? Thanks to let me know.

Kind regards,
Anne.


On 12 Jan 2010, at 12:33, Peter wrote:

> On Tue, Jan 12, 2010 at 10:27 AM, Peter <biopython at maubp.freeserve.co.uk 
> > wrote:
>> On Mon, Jan 11, 2010 at 5:32 PM, Anne Pajon <ap12 at sanger.ac.uk>  
>> wrote:
>>> Here is the diff between the EMBL output from Bio.SeqIO and the  
>>> genbank
>>> output from Bio.SeqIO converted with the EMBOSS tool to an EMBL  
>>> file:
>>>
>>> ...
>>>
>>> The main differences are on line breaks.
>>
>> I hadn't yet done a comparison against EMBOSS (what version do you
>> have), but yes, it looks like I am wrapping the feature tables  
>> using a
>> shorter line length - we should check that, and it would be easy to
>> adjust in Bio/SeqIO/InsdcIO.py
>
> The spec is pretty clear than the feature lines should be up to 80
> characters. The premature wrapping was because I had been
> testing length < 80 instead of <= 80, which is now fixed in git.
>
> Peter

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Dr Anne Pajon - Pathogen Genomics, Team 81
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