ENH: Added new action that can download AMRFinderPlus database called fetch_amrfinderplus_db

README.md

@@ -15,7 +15,7 @@ To install _q2-amr_, follow the steps described below.
 mamba create -yn q2-amr \
   -c https://packages.qiime2.org/qiime2/2024.2/shotgun/released/ \
   -c qiime2 -c conda-forge -c bioconda -c defaults \
-  qiime2 q2cli q2templates q2-types q2-feature-table q2-demux rgi tqdm
+  qiime2 q2cli q2templates q2-types q2-feature-table q2-demux rgi tqdm ncbi-amrfinderplus
 
 conda activate q2-amr
 
@@ -38,7 +38,7 @@ qiime info
 CONDA_SUBDIR=osx-64 mamba create -yn q2-amr \
   -c https://packages.qiime2.org/qiime2/2024.2/shotgun/released/ \
   -c qiime2 -c conda-forge -c bioconda -c defaults \
-  qiime2 q2cli q2templates q2-types q2-feature-table q2-demux rgi tqdm
+  qiime2 q2cli q2templates q2-types q2-feature-table q2-demux rgi tqdm ncbi-amrfinderplus
 
 conda activate q2-amr
 conda config --env --set subdir osx-64
@@ -57,19 +57,20 @@ qiime info
 
 ## Functionality
 This QIIME 2 plugin contains actions used to annotate short single/paired-end
-sequencing reads and MAGs with antimicrobial resistance genes. Currently, the [CARD](https://card.mcmaster.ca) database is supported  (for details on
-the implementation and usage, please refer to the [rgi](https://github.com/arpcard/rgi) documentation). Below you will
+sequencing reads and MAGs with antimicrobial resistance genes. Currently, the tools [RGI](https://github.com/arpcard/rgi) and [AMRFinderPlus](https://github.com/ncbi/amr) are supported (for details on
+the implementation and usage, please refer to the documentation of the tools). Below you will
 find an overview of actions available in the plugin.
 
-| Action                | Description                                                                          | Underlying tool                       | Used function                        |
-|-----------------------|--------------------------------------------------------------------------------------|---------------------------------------|--------------------------------------|
-| fetch-card-db         | Download and preprocess CARD and WildCARD data.                                      | [rgi](https://github.com/arpcard/rgi) | card_annotation, wildcard_annotation |
-| annotate-mags-card    | Annotate MAGs with antimicrobial resistance gene information from CARD.              | [rgi](https://github.com/arpcard/rgi) | main, load                           |
-| annotate-reads-card   | Annotate metagenomic reads with antimicrobial resistance gene information from CARD. | [rgi](https://github.com/arpcard/rgi) | bwt, load                            |
-| heatmap               | Create a heatmap from annotate-mags-card output files.                               | [rgi](https://github.com/arpcard/rgi) | heatmap                              |
-| kmer-query-mags-card  | Pathogen-of-origin prediction for ARGs in MAGs.                                      | [rgi](https://github.com/arpcard/rgi) | kmer-query, load                     |
-| kmer-query-reads-card | Pathogen-of-origin prediction for ARGs in reads.                                     | [rgi](https://github.com/arpcard/rgi) | kmer-query, load                     |
-| kmer-build-card       | Build a kmer database with a custom kmer length.                                     | [rgi](https://github.com/arpcard/rgi) | kmer-build                           |
+| Action                  | Description                                                                          | Underlying tool                              | Used function                        |
+|-------------------------|--------------------------------------------------------------------------------------|----------------------------------------------|--------------------------------------|
+| fetch-card-db           | Download and preprocess CARD and WildCARD data.                                      | [rgi](https://github.com/arpcard/rgi)        | card_annotation, wildcard_annotation |
+| annotate-mags-card      | Annotate MAGs with antimicrobial resistance gene information from CARD.              | [rgi](https://github.com/arpcard/rgi)        | main, load                           |
+| annotate-reads-card     | Annotate metagenomic reads with antimicrobial resistance gene information from CARD. | [rgi](https://github.com/arpcard/rgi)        | bwt, load                            |
+| heatmap                 | Create a heatmap from annotate-mags-card output files.                               | [rgi](https://github.com/arpcard/rgi)        | heatmap                              |
+| kmer-query-mags-card    | Pathogen-of-origin prediction for ARGs in MAGs.                                      | [rgi](https://github.com/arpcard/rgi)        | kmer-query, load                     |
+| kmer-query-reads-card   | Pathogen-of-origin prediction for ARGs in reads.                                     | [rgi](https://github.com/arpcard/rgi)        | kmer-query, load                     |
+| kmer-build-card         | Build a kmer database with a custom kmer length.                                     | [rgi](https://github.com/arpcard/rgi)        | kmer-build                           |
+| fetch-amrfinderplus-db  | Download AMRFinderPlus database.                                                     | [AMRFinderPlus](https://github.com/ncbi/amr) | -u                                   |
 
 ## Dev environment
 This repository follows the _black_ code style. To make the development slightly easier

ci/recipe/meta.yaml

@@ -17,6 +17,7 @@ requirements:
     - setuptools
 
   run:
+    - ncbi-amrfinderplus
     - python=3.8.*
     - qiime2 {{ qiime2_epoch }}.*
     - q2-demux {{ qiime2_epoch }}.*

q2_amr/amrfinderplus/database.py

@@ -0,0 +1,50 @@
+import os
+import re
+import subprocess
+
+from qiime2.util import duplicate
+
+from q2_amr.amrfinderplus.types import AMRFinderPlusDatabaseDirFmt
+from q2_amr.card.utils import run_command
+
+
+def fetch_amrfinderplus_db() -> AMRFinderPlusDatabaseDirFmt:
+    amrfinderplus_db = AMRFinderPlusDatabaseDirFmt()
+
+    # Run "amrfinder -u" command that downloads the database
+    run_amrfinder_u()
+
+    # Define path where the database will be downloaded to
+    conda_prefix = os.getenv("CONDA_PREFIX")
+    amrfinder_db_path = os.path.join(
+        conda_prefix, "share", "amrfinderplus", "data", "latest"
+    )
+
+    # Copy all files from amrfinder_db_path to database directory format
+    _copy_all(amrfinder_db_path, amrfinderplus_db.path)
+
+    return amrfinderplus_db
+
+
+def _copy_all(src_dir, des_dir):
+    regex = re.compile(r".*(?:AMR_CDS|changes).*")
+    # Loop over all files in the source directory
+    for file in os.listdir(src_dir):
+        # Check if the filename does not match the regex pattern and copy the file
+        # from src to des. Files matching the pattern are not needed for the database.
+        if not regex.match(file):
+            duplicate(os.path.join(src_dir, file), os.path.join(des_dir, file))
+
+
+def run_amrfinder_u():
+    # The command "amrfinder -u" downloads the latest amrfinderplus database or
+    # updates it
+    cmd = ["amrfinder", "-u"]
+    try:
+        run_command(cmd, verbose=True)
+    except subprocess.CalledProcessError as e:
+        raise Exception(
+            "An error was encountered while running AMRFinderPlus, "
+            f"(return code {e.returncode}), please inspect "
+            "stdout and stderr to learn more."
+        )

q2_amr/amrfinderplus/tests/test_database.py

@@ -0,0 +1,52 @@
+import os
+import subprocess
+from unittest.mock import patch
+
+from qiime2.plugin.testing import TestPluginBase
+
+from q2_amr.amrfinderplus.database import (
+    _copy_all,
+    fetch_amrfinderplus_db,
+    run_amrfinder_u,
+)
+
+
+class TestFetchAMRFinderPlusDB(TestPluginBase):
+    package = "q2_amr.amrfinderplus.tests"
+
+    @patch("q2_amr.amrfinderplus.database.run_amrfinder_u")
+    @patch("q2_amr.amrfinderplus.database._copy_all")
+    def test_fetch_amrfinderplus_db(self, mock_run_amrfinder_u, mock__copy_all):
+        fetch_amrfinderplus_db()
+
+    @patch("q2_amr.amrfinderplus.database.run_command")
+    def test_run_amrfinder_u(self, mock_run_command):
+        run_amrfinder_u()
+        mock_run_command.assert_called_once_with(
+            ["amrfinder", "-u"],
+            verbose=True,
+        )
+
+    @patch("q2_amr.amrfinderplus.database.run_command")
+    def test_run_amrfinder_u_error(self, mock_run_command):
+        expected_message = (
+            "An error was encountered while running AMRFinderPlus, "
+            "(return code 1), please inspect stdout and stderr to learn more."
+        )
+        mock_run_command.side_effect = subprocess.CalledProcessError(1, "cmd")
+        with self.assertRaises(Exception) as cm:
+            run_amrfinder_u()
+        self.assertEqual(str(cm.exception), expected_message)
+
+    def test__copy_all(self):
+        tmp = self.temp_dir.name
+        os.mkdir(os.path.join(tmp, "src"))
+        os.mkdir(os.path.join(tmp, "des"))
+
+        with open(os.path.join(tmp, "src", "a"), "w"), open(
+            os.path.join(tmp, "src", "AMR_CDS.nto"), "w"
+        ):
+            pass
+
+        _copy_all(os.path.join(tmp, "src"), os.path.join(tmp, "des"))
+        self.assertTrue(os.path.exists(os.path.join(tmp, "des", "a")))

q2_amr/card/utils.py

@@ -16,7 +16,7 @@
 )
 
 
-def run_command(cmd, cwd, verbose=True):
+def run_command(cmd, cwd=None, verbose=True):
     if verbose:
         print(EXTERNAL_CMD_WARNING)
         print("\nCommand:", end=" ")

q2_amr/citations.bib

@@ -26,3 +26,14 @@ @article{alcock_card_2023
 	keywords = {*Data Curation, *Databases, Factual, *Drug Resistance, Microbial, *Machine Learning, Anti-Bacterial Agents/pharmacology, Genes, Bacterial, Likelihood Functions, Molecular Sequence Annotation, Software},
 	pages = {D690--D699},
 }
+
+@article{feldgarden2021amrfinderplus,
+  title={AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence},
+  author={Feldgarden, Michael and Brover, Vyacheslav and Gonzalez-Escalona, Narjol and Frye, Jonathan G and Haendiges, Julie and Haft, Daniel H and Hoffmann, Maria and Pettengill, James B and Prasad, Arjun B and Tillman, Glenn E and others},
+  journal={Scientific reports},
+  volume={11},
+  number={1},
+  pages={12728},
+  year={2021},
+  publisher={Nature Publishing Group UK London}
+}

q2_amr/plugin_setup.py

@@ -29,6 +29,7 @@
 from qiime2.plugin import Citations, Plugin
 
 from q2_amr import __version__
+from q2_amr.amrfinderplus.database import fetch_amrfinderplus_db
 from q2_amr.amrfinderplus.types._format import (
     AMRFinderPlusAnnotationDirFmt,
     AMRFinderPlusAnnotationFormat,
@@ -1080,6 +1081,20 @@
     " size",
     citations=[citations["alcock_card_2023"]],
 )
+plugin.methods.register_function(
+    function=fetch_amrfinderplus_db,
+    inputs={},
+    parameters={},
+    outputs=[("amrfinderplus_db", AMRFinderPlusDatabase)],
+    input_descriptions={},
+    parameter_descriptions={},
+    output_descriptions={
+        "amrfinderplus_db": "AMRFinderPlus database.",
+    },
+    name="Download AMRFinderPlus database.",
+    description="Download the latest version of the AMRFinderPlus database.",
+    citations=[citations["feldgarden2021amrfinderplus"]],
+)
 
 # Registrations
 plugin.register_semantic_types(