Raise an error if the codon usage table is not found for the given taxonomy ID

Edinburgh-Genome-Foundry / codon-usage-tables

:bar_chart: Codon usage tables in code-friendly format + Python bindings

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Raise an error if the codon usage table is not found for the given taxonomy ID #4

Closed lebolo closed 4 years ago

lebolo commented 4 years ago

No idea if this is still maintained, but it would be nice to raise an error when the usage table isn't available on the website.

I mainly wanted this feature in https://github.com/Edinburgh-Genome-Foundry/DnaChisel, but didn't see the custom python_codon_tables code in that repo (I believe you add a web_timeout there that isn't in this repo?).

Zulko commented 4 years ago

Quick remarks in case it's useful :

DNA Chisel used to have its own codon usage code, but it now uses python_codon_tables so the behavior should be the same in Chisel and here.
At some point I added a timeout to protect against kazusa.jp going down (which causes the library to hang indefinitely and is no fun at all), but that was some time ago and I changed machine since 😬 . Would be a nice one to (re)implement @veghp 🙃
There is currently no mechanism for when the TaxID is not on kazusa.jp so thanks very much for this fix!

veghp commented 4 years ago

Apparently the repo did not have the latest code, v0.1.9, as on PyPI. This explains why DNA Chisel was using a web_timeout. Updated now both the repo and PyPI to the latest version.

Zulko commented 4 years ago

:facepalm: sounds like my mess. Sorry for that Peter and kudos for spotting the problem!

On Sun, Sep 6, 2020 at 11:02 AM Peter Vegh notifications@github.com wrote:

Apparently the repo did not have the latest code, v0.1.9, as on PyPI. This explains why DNA Chisel was using a web_timeout. Updated now both the repo and PyPI to the latest version.

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