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ENH: Fetch NCBI Taxonomy Data (input to build_custom_diamond_db action) #107

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4 tasks done
Tracked by #119
Sann5 opened this issue Dec 18, 2023 · 0 comments · Fixed by #118
Closed
4 tasks done
Tracked by #119

ENH: Fetch NCBI Taxonomy Data (input to build_custom_diamond_db action) #107

Sann5 opened this issue Dec 18, 2023 · 0 comments · Fixed by #118
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enhancement New feature or request

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Sann5 commented Dec 18, 2023

Context

The build_custom_diamond_db action can optionally take a ReferenceDB[NCBITaxonomy] artifact, with which the resulting Diamond database contains taxonomy features. There is a need to create an action that produces this ReferenceDB[NCBITaxonomy] artifact by fetching the appropriate data from the internet.

Something like...

qiime moshpit fetch-ncbi-taxonomy-db ...

Important Considerations

There are two links from where the data comes from. One can find out the time and date of the last modification to the file on the server by calling wget -S --spider <somewhere_in_the_internet>. It might be important to include this data in the artifact since the version might influence the results.

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