Update MarkerScan for compatibility with v2 of the NCBI API#14
Merged
prototaxites merged 13 commits intoCobiontID:ncbi_fixfrom Nov 6, 2025
Merged
Update MarkerScan for compatibility with v2 of the NCBI API#14prototaxites merged 13 commits intoCobiontID:ncbi_fixfrom
prototaxites merged 13 commits intoCobiontID:ncbi_fixfrom
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- use lightweight custom class reimplementing required functionality with the NCBI API - tidy up some logic with counting loops by just returning counts from the API - use a bit of pathlib to do some path stuff - re-format modified scripts with Ruff
…ersion of snakemake
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The primary function of this PR is to update MarkerScan to be compatible with v2 of the NCBI API, replacing the dependency on
ncbi-datasets-pylibwhich is deprecated.To do this, I have added a small class in
scripts/NcbiApi.pywhich replicates the required functionality using therequestslibrary. In implementing this into the various scripts, I've also made a few changes to improve efficiency, including determining the number of assemblies directly from the API rather than counting them in a loop.In order to run, currently you must set the environment variable NCBI_API_KEY in order to access the API. I don't know enough Snakemake to modify the Snakefile, but I've also added command-line arguments (
-k) to the affected Python scripts to allow this to be specified manually.In trying to get the modified version of the pipeline to run, I have also made a number of small changes:
map-hifioption used in the pipeline (are there an alternate set of env files somewhere?)