Genbank tm shorthand unknown

[a-lewis-acid]

When I submit an annotated Genbank file to the API with an annotation to constrain the melting temperature of a region it returns "Program error: Unknown specification tm".

E.g. @tm(50-55C)

Is this a bug or is the tm specification meant to be used in a different way to that described in the API notes?

[veghp]

Thank you for bringing attention to this, I managed to reproduce this issue (probably EnforceMeltingTemperature is missing from https://github.com/Edinburgh-Genome-Foundry/DnaChisel/blob/master/dnachisel/builtin_specifications/__init__.py#L58 or along those lines). I'll address this in the coming days.

[a-lewis-acid]

Thank you for looking into this.

Does the web app require the dev branch to be merged into the master branch for the fix to take effect?

[veghp]

Yes it needs to be merged, but more importantly the website needs to be built again. For that I'll have to update the website code and packages as well, so it will take quite some time unfortunately..

[Zulko]

If the app update is a blocker, note that pip install dnachisel[reports] installs everything needed to do the same as the web app, in particular it installs a CLI that accepts annotated genbanks:

>>> dnachisel annotated_record.gb optimization_report/

So this would just require a new pypi release with the fix (or installing from the dev branch).

[veghp]

Yes, I can make a new release (probably only next week though).