[Biopython] Support for Xdna, SnapGene and GCK formats

Peter Cock p.j.a.cock at googlemail.com
Wed Jul 31 11:25:28 UTC 2019


Hello Damien,

Apologies that your past emails didn't reach me. I wonder if anyone else did
see them (and then f this is happening to anyone else)? This is really
frustrating,
but following our discussion on Twitter, I can still see your original and new
emails to the mailing list on the archive - but not in my GMail, not even in
the spam folder:

https://mailman.open-bio.org/pipermail/biopython/2018-December/016574.html
https://mailman.open-bio.org/pipermail/biopython/2019-July/016647.html
https://mailman.open-bio.org/pipermail/biopython/2019-July/016648.html

https://twitter.com/gouttegd/status/1156170774329380864

I've not used any of the tools and their formats, but this still seems
like a good
fit for Biopython's SeqIO:

"Xdna" format, used by DNA  Strider and Serial Cloner:
http://serialbasics.free.fr/Serial_Cloner.html

SnapGene format:
https://www.snapgene.com/

"GCK" format, used by  Gene Construction Kit:
http://www.textco.com/gene-construction-kit.php

Damian's code is here:

https://git.incenp.org/damien/binseqs/src/branch/master/incenp/bio/seqio

Note we'd ask you to dual license this, as done here for example:

https://github.com/biopython/biopython/blob/master/Bio/SeqRecord.py

Also some minimal tests would be needed - are you able to share at least one
small file in each new format? And are you testing on both Python 2.7 and 3.x?

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

Thank you for your patience!

Peter


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