[Biopython] Support for Xdna, SnapGene and GCK formats

[Peter Cock]

On Wed, Jul 31, 2019 at 8:11 PM Damien Goutte-Gattat
<dgouttegattat at incenp.org> wrote:
>
> 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.

Great.

> >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.

Great.

> 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.

The website [1] had a fairly liberal copyright statement at the bottom,
suggesting a sample file could be used with attribution (e.g. in the git
check in comment and where the test or example code used it)?

> > 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.

Perfect. That should make things smoother.

> >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.

One of the main contributors Michiel de Hoon uses Yahoo, so that could
very well be a problem for other posters.

Damien, you evidently know a lot more about email headers etc than me.
Are you also familiar with mailman, and how it might be better configured
on this specific point?

We (the OBF) intend to migrate the current self hosted mailman instance
to paid hosting in part because we don't have enough volunteer administrators
to keep in top condition - sadly even making that happen requires a large
chunk of time from a handful of the existing team and hasn't happened yet:

https://www.open-bio.org/2017/12/15/mailing-list-consolidation/

Peter

>
> [1]
> https://emb.carnegiescience.edu/drosophila-gateway-vector-collection#_Vector_sequence_files
>
> [2] https://tools.ietf.org/html/rfc7960#section-4.1.3.3