[Biopython] Support for Xdna, SnapGene and GCK formats

Wed Jul 31 19:11:19 UTC 2019

Hi Peter and Biopython folks,

On Wed, Jul 31, 2019 at 12:25:28PM +0100, Peter Cock wrote:
>I've not used any of the tools and their formats, but this still seems
>like a good fit for Biopython's SeqIO:

Thank you for your interest.

>Note we'd ask you to dual license this, as done here for example:
>
>https://github.com/biopython/biopython/blob/master/Bio/SeqRecord.py

I noticed that. My code is currently under a 1-clause BSD-like license, 
but as I am the only author, I can easily change that to the terms used 
by Biopython.

>Also some minimal tests would be needed - are you able to share at 
>least one small file in each new format?

I can generate sample files in the "Xdna" and SnapGene formats at will.  
However I don't have access to any version of Gene Construction Kit and 
cannot generate new files in the GCK format.

All the GCK files I have come from the "Drosophila Gateway Vector 
Collection" [1]; those files are not explicitly released under any free 
license (in fact there are no license terms at all), so I don't think we 
could bundle even one of them with the Biopython's source code, even if 
it is just to serve as a test file.

> And are you testing on both Python 2.7 and 3.x?

Yes. I try to make sure the code is running correctly under Python 2.7, 
3.5, and 3.7.

>If that all seems fine, I look forward to a pull request.

Great. I'll work on that in the next few days.

Cheers,

- Damien

P.S.:

>Apologies that your past emails didn't reach me.

I believe this was due to the fact that the mailing list software was 
modifying my messages (thereby invalidating the DKIM signatures) without 
taking ownership of said messages, as is now recommended [2].  Since the 
DMARC policy of my domain was set to "reject", DMARC-compliant mail 
servers (such as GMail's) rejected my messages outright.

I have now relaxed my DMARC policy, which should prevent that issue from 
happening again.

Of note, I suspect anyone sending mail to this mailing list using an 
address from a mail service provider with a strict DMARC policy (such as 
Yahoo) will encounter the same problem.

- D

[1] 
https://emb.carnegiescience.edu/drosophila-gateway-vector-collection#_Vector_sequence_files

[2] https://tools.ietf.org/html/rfc7960#section-4.1.3.3
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