[Biopython] Support for Xdna, SnapGene and GCK formats
Damien Goutte-Gattat
dgouttegattat at incenp.org
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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