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v3.1.8 - Improved biomarkers report consistency

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@kbessonov1984 kbessonov1984 released this 11 Dec 16:51
· 5 commits to master since this release

This release includes small but important convenience fixes such as fix to #152 issue where in cases when there are absolutely no plasmid biomarkers (i.e. empty biomarkers report) mob_typer would fail. Additionally, this release improves marker reporting consistency between biomarkers and the main plasmid typing reports generated by mob_recon and mob_typer. The biomarkers report introduced since v3.1.7 lists the main plasmid biomarkers and their coordinates. Finally, plasmid databases were cleaned, synced and redundant files removed. A new databases archive url was updated and now points to https://zenodo.org/records/10304948/files/data.tar.gz?download=1

  • Fixed permanently issue #152 and added a unit test test_mob_recon_no_plasmid_biomarkers()
  • Updated the core database archive data.tar.gz: a) removed redundant host_range_ncbirefseq_plasmidDB.txt and host_range_ncbirefseq_plasmidDB.csv; b) updated clusters.txt with new mob_typer biomarker results for consistency (the cluster codes and number of records did not change)
  • Improved biomarkers report consistency with other reports by making sure that all markers listed in the mob_typer report are present in the biomarkers report. Implemented a new unit tests listed in test_databases_consistency.py