Merge pull request #221 from phac-nml/development

Merging Development into Main (v0.11.0 Release)

.github/workflows/ci-test.yml

@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
 
     env:
-      DATABASE_COMMITS: '--resfinder-commit fa32d9a3cf0c12ec70ca4e90c45c0d590ee810bd --pointfinder-commit 8c694b9f336153e6d618b897b3b4930961521eb8 --plasmidfinder-commit c18e08c17a5988d4f075fc1171636e47546a323d'
+      DATABASE_COMMITS: '--resfinder-commit d1e607b8989260c7b6a3fbce8fa3204ecfc09022 --pointfinder-commit 694919f59a38980204009e7ade76bf319cb7df0b --plasmidfinder-commit c18e08c17a5988d4f075fc1171636e47546a323d'
 
     strategy:
       fail-fast: False
@@ -61,4 +61,6 @@ jobs:
 
       - name: Run Tests
         shell: bash -l {0}
-        run: python setup.py test
+        run: |
+          pip install pytest
+          pytest

CHANGELOG.md

@@ -1,3 +1,11 @@
+# Version 0.11.0
+
+* Updated the Resfinder database to use the 2024-08-06 release.
+* Updated the Pointfinder database to use the 2024-08-08 release.
+* The Resfinder and Pointfinder databases now use FASTA record IDs with accession numbers (ex: `pmrA` -> `pmrA_1_CP055130.1`). StarAMR has been updated to support this, but database backwards compatibility is unlikely.
+* The `genes_to_exclude` is affected by the above change and must now use gene IDs that exactly match the new FASTA record IDs with accession IDs.
+* Removed ARG drug key entries with "None" or missing resistance.
+
 # Version 0.10.0
 
 * Updated the Plasmidfinder database to use the January 18th 2023 release.

README.md

@@ -145,7 +145,7 @@ If you wish to update to the latest ResFinder, PointFinder, and PlasmidFinder da
 staramr db update --update-default
 ```
 
-If you wish to switch to specific git commits of either ResFinder, PointFinder, or PlasmidFinder databases you may also pass `--resfinder-commit [COMMIT]`, `--pointfinder-commit [COMMIT]`, and `--plasmidfinder-commit [COMMIT]`.
+If you wish to switch to specific git commits of either ResFinder, PointFinder, or PlasmidFinder databases you may also pass `--resfinder-commit [COMMIT]`, `--pointfinder-commit [COMMIT]`, and `--plasmidfinder-commit [COMMIT]`. However, please note that because of compatibility issues arising from changes in the source databases, this functionality is largely unsupported and is unlikely to work for versions of the databases that StarAMR wasn't released with.
 
 ## Restore Database
 
@@ -245,11 +245,11 @@ By default, the ResFinder/PointFinder/PlasmidFinder genes listed in [genes_to_ex
 
 ```
 gene_id
-aac(6')-Iaa_1_NC_003197
-ColpVC_1__JX133088
+gyrA_1_CP073768.1
+pmrB_1_CP051284.1
 ```
 
-Please make sure to include `gene_id` in the first line. The default exclusion list can also be disabled with `--no-exclude-genes`.
+Please make sure to include `gene_id` in the first line. The default exclusion list can also be disabled with `--no-exclude-genes`. Gene IDs must exactly match the FASTA record IDs provided in the source databases.
 
 ## Complex Mutations
 
@@ -504,7 +504,7 @@ Restores the default database for `staramr`.
 
 # Caveats
 
-This software is still a work-in-progress.  In particular, not all organisms stored in the PointFinder database are supported (only *salmonella*, *campylobacter* are currently supported). Additionally, the predicted phenotypes are for microbiological resistance and *not* clinical resistance. Phenotype/drug resistance predictions are an experimental feature which is continually being improved.
+This software is still a work-in-progress.  In particular, not all organisms stored in the PointFinder database are supported (only *enterococcus_faecalis*, *helicobacter_pylori*, *enterococcus_faecium*, *campylobacter*, *escherichia_coli*, *salmonella* are currently supported). Additionally, the predicted phenotypes are for microbiological resistance and *not* clinical resistance. Phenotype/drug resistance predictions are an experimental feature which is continually being improved.
 
 `staramr` only works on assembled genomes and not directly on reads. A quick genome assembler you could use is [Shovill][shovill]. Or, you may also wish to try out the [ResFinder webservice][resfinder-web],  or the command-line tools [rgi][] or [ariba][] which will work on sequence reads as well as genome assemblies.  You may also wish to check out the [CARD webservice][card-web]. 
 

scripts/data-conversion/pointfinder-drug-resistance.ipynb

@@ -17,7 +17,7 @@
     {
      "data": {
       "text/plain": [
-       "dict_keys(['Salmonella', 'Shigella E. coli', 'Campylobacter'])"
+       "dict_keys(['Salmonella', 'Shigella E. coli', 'Campylobacter', 'NCBI AMRfinder'])"
       ]
      },
      "execution_count": 1,
@@ -28,7 +28,7 @@
    "source": [
     "import pandas as pd\n",
     "\n",
-    "pointfinder_file = '../../drug-key-update/pointfinder 072621.xlsx'\n",
+    "pointfinder_file = '../../pointfinder.xlsx'\n",
     "\n",
     "pointfinder_excel = pd.ExcelFile(pointfinder_file)\n",
     "sheets_df_map_orig = {n: pd.read_excel(pointfinder_excel, sheet_name=n, header=None) for n in pointfinder_excel.sheet_names}\n",
@@ -407,6 +407,14 @@
    "source": [
     "pointfinder_df_reduced.to_csv('../../staramr/databases/resistance/data/ARG_drug_key_pointfinder.tsv', sep='\\t', index=False)"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "938df9d4-d16a-4855-aee0-5208fadfad68",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
@@ -425,7 +433,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.4"
+   "version": "3.12.3"
   }
  },
  "nbformat": 4,