[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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