diff --git a/.coveragerc b/.coveragerc index 4776ee2..ab586bc 100644 --- a/.coveragerc +++ b/.coveragerc @@ -1,10 +1,10 @@ [run] -source=q2_amr +source=q2_rgi branch = True omit = */tests* */__init__.py - q2_amr/_version.py + q2_rgi/_version.py versioneer.py [report] @@ -12,5 +12,5 @@ fail_under = 90 omit = */tests* */__init__.py - q2_amr/_version.py + q2_rgi/_version.py versioneer.py diff --git a/.gitattributes b/.gitattributes index 3148fe6..606e4db 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1 +1 @@ -q2_amr/_version.py export-subst +q2_rgi/_version.py export-subst diff --git a/.gitignore b/.gitignore index b85dd07..b4c4d79 100644 --- a/.gitignore +++ b/.gitignore @@ -131,6 +131,6 @@ dmypy.json # PyCharm configuration .idea/ -/q2_amr/charts_testing.py +/q2_rgi/charts_testing.py /index.html /bwt_test_file.py diff --git a/MANIFEST.in b/MANIFEST.in index 6571d72..75dcc02 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,2 +1,2 @@ include versioneer.py -include q2_amr/_version.py +include q2_rgi/_version.py diff --git a/README.md b/README.md index ca81dbd..514014b 100644 --- a/README.md +++ b/README.md @@ -1,27 +1,27 @@ -# q2-amr -![CI](https://github.com/bokulich-lab/q2-amr/actions/workflows/ci-dev.yaml/badge.svg) -[![codecov](https://codecov.io/gh/bokulich-lab/q2-amr/branch/main/graph/badge.svg?token=THMBOFUZR0)](https://codecov.io/gh/bokulich-lab/q2-amr) +# q2-rgi +![CI](https://github.com/bokulich-lab/q2-rgi/actions/workflows/ci-dev.yaml/badge.svg) +[![codecov](https://codecov.io/gh/bokulich-lab/q2-rgi/branch/main/graph/badge.svg?token=THMBOFUZR0)](https://codecov.io/gh/bokulich-lab/q2-rgi) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) QIIME 2 plugin for antimicrobial resistance gene annotation of MAGs and metagenomic reads. ## Installation -To install _q2-amr_, follow the steps described below. +To install _q2-rgi_, follow the steps described below.
macOS (intel) / Linux ```shell -mamba create -yn q2-amr \ +mamba create -yn q2-rgi \ -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 -conda activate q2-amr +conda activate q2-rgi pip install --no-deps --force-reinstall \ git+https://github.com/misialq/rgi.git@py38-fix \ - git+https://github.com/bokulich-lab/q2-amr.git + git+https://github.com/bokulich-lab/q2-rgi.git ``` Refresh cache and check that everything worked: @@ -35,17 +35,17 @@ qiime info macOS (apple silicon) ```shell -CONDA_SUBDIR=osx-64 mamba create -yn q2-amr \ +CONDA_SUBDIR=osx-64 mamba create -yn q2-rgi \ -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 -conda activate q2-amr +conda activate q2-rgi conda config --env --set subdir osx-64 pip install --no-deps --force-reinstall \ git+https://github.com/misialq/rgi.git@py38-fix \ - git+https://github.com/bokulich-lab/q2-amr.git + git+https://github.com/bokulich-lab/q2-rgi.git ``` Refresh cache and check that everything worked: @@ -58,18 +58,18 @@ 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 +the implementation and usage, please refer to the [rgi](https://github.com/arpcard/rgi) documentation). 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 | +| 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 | ## Dev environment This repository follows the _black_ code style. To make the development slightly easier diff --git a/ci/recipe/meta.yaml b/ci/recipe/meta.yaml index 97fc1bd..303d3c1 100644 --- a/ci/recipe/meta.yaml +++ b/ci/recipe/meta.yaml @@ -2,7 +2,7 @@ {% set version = data.get('version') or 'placehold' %} package: - name: q2-amr + name: q2-rgi version: {{ version }} source: @@ -32,12 +32,12 @@ test: - coverage - pytest-cov imports: - - q2_amr + - q2_rgi - qiime2.plugins.amr commands: - - pytest --cov q2_amr --cov-report xml:coverage.xml --pyargs q2_amr + - pytest --cov q2_rgi --cov-report xml:coverage.xml --pyargs q2_rgi about: - home: https://github.com/bokulich-lab/q2-amr + home: https://github.com/bokulich-lab/q2-rgi license: BSD-3-Clause license_family: BSD diff --git a/q2_amr/__init__.py b/q2_rgi/__init__.py similarity index 87% rename from q2_amr/__init__.py rename to q2_rgi/__init__.py index 131978b..f335818 100644 --- a/q2_amr/__init__.py +++ b/q2_rgi/__init__.py @@ -5,6 +5,10 @@ # # The full license is in the file LICENSE, distributed with this software. # ---------------------------------------------------------------------------- +import importlib + from . import _version __version__ = _version.get_versions()["version"] + +importlib.import_module("q2_rgi.types") diff --git a/q2_amr/_version.py b/q2_rgi/_version.py similarity index 99% rename from q2_amr/_version.py rename to q2_rgi/_version.py index 5095c93..d160c7e 100644 --- a/q2_amr/_version.py +++ b/q2_rgi/_version.py @@ -45,8 +45,8 @@ def get_config(): cfg.VCS = "git" cfg.style = "pep440" cfg.tag_prefix = "" - cfg.parentdir_prefix = "q2-amr-" - cfg.versionfile_source = "q2_amr/_version.py" + cfg.parentdir_prefix = "q2-rgi-" + cfg.versionfile_source = "q2_rgi/_version.py" cfg.verbose = False return cfg diff --git a/q2_amr/assets/rgi/heatmap/index.html b/q2_rgi/assets/rgi/heatmap/index.html similarity index 100% rename from q2_amr/assets/rgi/heatmap/index.html rename to q2_rgi/assets/rgi/heatmap/index.html diff --git a/q2_amr/card/__init__.py b/q2_rgi/card/__init__.py similarity index 100% rename from q2_amr/card/__init__.py rename to q2_rgi/card/__init__.py diff --git a/q2_amr/card/database.py b/q2_rgi/card/database.py similarity index 98% rename from q2_amr/card/database.py rename to q2_rgi/card/database.py index 766f9df..e4089bb 100644 --- a/q2_amr/card/database.py +++ b/q2_rgi/card/database.py @@ -9,8 +9,8 @@ import requests from tqdm import tqdm -from q2_amr.card.utils import colorify, run_command -from q2_amr.types._format import ( +from q2_rgi.card.utils import colorify, run_command +from q2_rgi.types._format import ( CARDDatabaseDirectoryFormat, CARDKmerDatabaseDirectoryFormat, ) diff --git a/q2_amr/card/heatmap.py b/q2_rgi/card/heatmap.py similarity index 95% rename from q2_amr/card/heatmap.py rename to q2_rgi/card/heatmap.py index b6c93ed..7b128a9 100644 --- a/q2_amr/card/heatmap.py +++ b/q2_rgi/card/heatmap.py @@ -8,8 +8,8 @@ import pkg_resources import q2templates -from q2_amr.card.utils import run_command -from q2_amr.types import CARDAnnotationDirectoryFormat +from q2_rgi.card.utils import run_command +from q2_rgi.types import CARDAnnotationDirectoryFormat def heatmap( @@ -20,7 +20,7 @@ def heatmap( display: str = "plain", frequency: bool = False, ): - TEMPLATES = pkg_resources.resource_filename("q2_amr", "assets") + TEMPLATES = pkg_resources.resource_filename("q2_rgi", "assets") annotation_dir = str(amr_annotation) with tempfile.TemporaryDirectory() as tmp: # Create directories for the JSON annotation files and the heatmap output files diff --git a/q2_amr/card/kmer.py b/q2_rgi/card/kmer.py similarity index 99% rename from q2_amr/card/kmer.py rename to q2_rgi/card/kmer.py index cb33d4f..3ea3d12 100644 --- a/q2_amr/card/kmer.py +++ b/q2_rgi/card/kmer.py @@ -7,8 +7,8 @@ import warnings from pathlib import Path -from q2_amr.card.utils import load_card_db, run_command -from q2_amr.types import ( +from q2_rgi.card.utils import load_card_db, run_command +from q2_rgi.types import ( CARDAlleleAnnotationDirectoryFormat, CARDAnnotationDirectoryFormat, CARDDatabaseDirectoryFormat, diff --git a/q2_amr/card/mags.py b/q2_rgi/card/mags.py similarity index 95% rename from q2_amr/card/mags.py rename to q2_rgi/card/mags.py index 7c0dbcf..83cad00 100644 --- a/q2_amr/card/mags.py +++ b/q2_rgi/card/mags.py @@ -6,8 +6,8 @@ import pandas as pd from q2_types.per_sample_sequences import MultiMAGSequencesDirFmt -from q2_amr.card.utils import create_count_table, load_card_db, read_in_txt, run_command -from q2_amr.types import CARDAnnotationDirectoryFormat, CARDDatabaseDirectoryFormat +from q2_rgi.card.utils import create_count_table, load_card_db, read_in_txt, run_command +from q2_rgi.types import CARDAnnotationDirectoryFormat, CARDDatabaseDirectoryFormat def annotate_mags_card( diff --git a/q2_amr/card/partition.py b/q2_rgi/card/partition.py similarity index 99% rename from q2_amr/card/partition.py rename to q2_rgi/card/partition.py index 50e4479..3c755fe 100644 --- a/q2_amr/card/partition.py +++ b/q2_rgi/card/partition.py @@ -5,8 +5,8 @@ import numpy as np from qiime2.util import duplicate -from q2_amr.card.utils import copy_files -from q2_amr.types import ( +from q2_rgi.card.utils import copy_files +from q2_rgi.types import ( CARDAlleleAnnotationDirectoryFormat, CARDAnnotationDirectoryFormat, CARDGeneAnnotationDirectoryFormat, diff --git a/q2_amr/card/reads.py b/q2_rgi/card/reads.py similarity index 98% rename from q2_amr/card/reads.py rename to q2_rgi/card/reads.py index f99c0c9..eea2aad 100644 --- a/q2_amr/card/reads.py +++ b/q2_rgi/card/reads.py @@ -13,8 +13,8 @@ ) from q2_types.sample_data import SampleData -from q2_amr.card.utils import create_count_table, load_card_db, read_in_txt, run_command -from q2_amr.types import ( +from q2_rgi.card.utils import create_count_table, load_card_db, read_in_txt, run_command +from q2_rgi.types import ( CARDAlleleAnnotationDirectoryFormat, CARDDatabaseDirectoryFormat, CARDGeneAnnotationDirectoryFormat, diff --git a/q2_amr/card/tests/__init__.py b/q2_rgi/card/tests/__init__.py similarity index 100% rename from q2_amr/card/tests/__init__.py rename to q2_rgi/card/tests/__init__.py diff --git a/q2_amr/card/tests/data/DNA_fasta.fasta b/q2_rgi/card/tests/data/DNA_fasta.fasta similarity index 100% rename from q2_amr/card/tests/data/DNA_fasta.fasta rename to q2_rgi/card/tests/data/DNA_fasta.fasta diff --git a/q2_amr/card/tests/data/DNA_fasta_-.fasta b/q2_rgi/card/tests/data/DNA_fasta_-.fasta similarity index 100% rename from q2_amr/card/tests/data/DNA_fasta_-.fasta rename to q2_rgi/card/tests/data/DNA_fasta_-.fasta diff --git a/q2_amr/card/tests/data/MANIFEST_mags b/q2_rgi/card/tests/data/MANIFEST_mags similarity index 100% rename from q2_amr/card/tests/data/MANIFEST_mags rename to q2_rgi/card/tests/data/MANIFEST_mags diff --git a/q2_amr/card/tests/data/MANIFEST_reads_paired b/q2_rgi/card/tests/data/MANIFEST_reads_paired similarity index 100% rename from q2_amr/card/tests/data/MANIFEST_reads_paired rename to q2_rgi/card/tests/data/MANIFEST_reads_paired diff --git a/q2_amr/card/tests/data/MANIFEST_reads_single b/q2_rgi/card/tests/data/MANIFEST_reads_single similarity index 100% rename from q2_amr/card/tests/data/MANIFEST_reads_single rename to q2_rgi/card/tests/data/MANIFEST_reads_single diff --git a/q2_amr/card/tests/data/card.tar.bz2 b/q2_rgi/card/tests/data/card.tar.bz2 similarity index 100% rename from q2_amr/card/tests/data/card.tar.bz2 rename to q2_rgi/card/tests/data/card.tar.bz2 diff --git a/q2_amr/card/tests/data/card_test.json b/q2_rgi/card/tests/data/card_test.json similarity index 100% rename from q2_amr/card/tests/data/card_test.json rename to q2_rgi/card/tests/data/card_test.json diff --git a/q2_amr/card/tests/data/collated/card_allele_annotation/sample1/allele_mapping_data.txt b/q2_rgi/card/tests/data/collated/card_allele_annotation/sample1/allele_mapping_data.txt similarity index 100% rename from q2_amr/card/tests/data/collated/card_allele_annotation/sample1/allele_mapping_data.txt rename to q2_rgi/card/tests/data/collated/card_allele_annotation/sample1/allele_mapping_data.txt diff --git a/q2_amr/card/tests/data/collated/card_allele_annotation/sample1/overall_mapping_stats.txt b/q2_rgi/card/tests/data/collated/card_allele_annotation/sample1/overall_mapping_stats.txt similarity index 100% rename from q2_amr/card/tests/data/collated/card_allele_annotation/sample1/overall_mapping_stats.txt rename to q2_rgi/card/tests/data/collated/card_allele_annotation/sample1/overall_mapping_stats.txt diff --git a/q2_amr/card/tests/data/collated/card_allele_annotation/sample1/sorted.length_100.bam b/q2_rgi/card/tests/data/collated/card_allele_annotation/sample1/sorted.length_100.bam similarity index 100% rename from q2_amr/card/tests/data/collated/card_allele_annotation/sample1/sorted.length_100.bam rename to q2_rgi/card/tests/data/collated/card_allele_annotation/sample1/sorted.length_100.bam diff --git a/q2_amr/card/tests/data/collated/card_allele_annotation/sample2/allele_mapping_data.txt b/q2_rgi/card/tests/data/collated/card_allele_annotation/sample2/allele_mapping_data.txt similarity index 100% rename from q2_amr/card/tests/data/collated/card_allele_annotation/sample2/allele_mapping_data.txt rename to q2_rgi/card/tests/data/collated/card_allele_annotation/sample2/allele_mapping_data.txt diff --git a/q2_amr/card/tests/data/collated/card_allele_annotation/sample2/overall_mapping_stats.txt b/q2_rgi/card/tests/data/collated/card_allele_annotation/sample2/overall_mapping_stats.txt similarity index 100% rename from q2_amr/card/tests/data/collated/card_allele_annotation/sample2/overall_mapping_stats.txt rename to q2_rgi/card/tests/data/collated/card_allele_annotation/sample2/overall_mapping_stats.txt diff --git a/q2_amr/card/tests/data/collated/card_allele_annotation/sample2/sorted.length_100.bam b/q2_rgi/card/tests/data/collated/card_allele_annotation/sample2/sorted.length_100.bam similarity index 100% rename from q2_amr/card/tests/data/collated/card_allele_annotation/sample2/sorted.length_100.bam rename to q2_rgi/card/tests/data/collated/card_allele_annotation/sample2/sorted.length_100.bam diff --git a/q2_amr/card/tests/data/collated/card_annotation/sample1/e026af61-d911-4de3-a957-7e8bf837f30d/amr_annotation.json b/q2_rgi/card/tests/data/collated/card_annotation/sample1/e026af61-d911-4de3-a957-7e8bf837f30d/amr_annotation.json similarity index 100% rename from q2_amr/card/tests/data/collated/card_annotation/sample1/e026af61-d911-4de3-a957-7e8bf837f30d/amr_annotation.json rename to q2_rgi/card/tests/data/collated/card_annotation/sample1/e026af61-d911-4de3-a957-7e8bf837f30d/amr_annotation.json diff --git a/q2_amr/card/tests/data/collated/card_annotation/sample1/e026af61-d911-4de3-a957-7e8bf837f30d/amr_annotation.txt b/q2_rgi/card/tests/data/collated/card_annotation/sample1/e026af61-d911-4de3-a957-7e8bf837f30d/amr_annotation.txt similarity index 100% rename from q2_amr/card/tests/data/collated/card_annotation/sample1/e026af61-d911-4de3-a957-7e8bf837f30d/amr_annotation.txt rename to q2_rgi/card/tests/data/collated/card_annotation/sample1/e026af61-d911-4de3-a957-7e8bf837f30d/amr_annotation.txt diff --git a/q2_amr/card/tests/data/collated/card_annotation/sample2/aa447c99-ecd9-4c4a-a53b-4df6999815dd/amr_annotation.json b/q2_rgi/card/tests/data/collated/card_annotation/sample2/aa447c99-ecd9-4c4a-a53b-4df6999815dd/amr_annotation.json similarity index 100% rename from q2_amr/card/tests/data/collated/card_annotation/sample2/aa447c99-ecd9-4c4a-a53b-4df6999815dd/amr_annotation.json rename to q2_rgi/card/tests/data/collated/card_annotation/sample2/aa447c99-ecd9-4c4a-a53b-4df6999815dd/amr_annotation.json diff --git a/q2_amr/card/tests/data/collated/card_annotation/sample2/aa447c99-ecd9-4c4a-a53b-4df6999815dd/amr_annotation.txt b/q2_rgi/card/tests/data/collated/card_annotation/sample2/aa447c99-ecd9-4c4a-a53b-4df6999815dd/amr_annotation.txt similarity index 100% rename from q2_amr/card/tests/data/collated/card_annotation/sample2/aa447c99-ecd9-4c4a-a53b-4df6999815dd/amr_annotation.txt rename to q2_rgi/card/tests/data/collated/card_annotation/sample2/aa447c99-ecd9-4c4a-a53b-4df6999815dd/amr_annotation.txt diff --git a/q2_amr/card/tests/data/collated/card_annotation/sample2/f5a16381-ea80-49f9-875e-620f333a9293/amr_annotation.json b/q2_rgi/card/tests/data/collated/card_annotation/sample2/f5a16381-ea80-49f9-875e-620f333a9293/amr_annotation.json similarity index 100% rename from q2_amr/card/tests/data/collated/card_annotation/sample2/f5a16381-ea80-49f9-875e-620f333a9293/amr_annotation.json rename to q2_rgi/card/tests/data/collated/card_annotation/sample2/f5a16381-ea80-49f9-875e-620f333a9293/amr_annotation.json diff --git a/q2_amr/card/tests/data/collated/card_annotation/sample2/f5a16381-ea80-49f9-875e-620f333a9293/amr_annotation.txt b/q2_rgi/card/tests/data/collated/card_annotation/sample2/f5a16381-ea80-49f9-875e-620f333a9293/amr_annotation.txt similarity index 100% rename from q2_amr/card/tests/data/collated/card_annotation/sample2/f5a16381-ea80-49f9-875e-620f333a9293/amr_annotation.txt rename to q2_rgi/card/tests/data/collated/card_annotation/sample2/f5a16381-ea80-49f9-875e-620f333a9293/amr_annotation.txt diff --git a/q2_amr/card/tests/data/collated/card_gene_annotation/sample1/gene_mapping_data.txt b/q2_rgi/card/tests/data/collated/card_gene_annotation/sample1/gene_mapping_data.txt similarity index 100% rename from q2_amr/card/tests/data/collated/card_gene_annotation/sample1/gene_mapping_data.txt rename to q2_rgi/card/tests/data/collated/card_gene_annotation/sample1/gene_mapping_data.txt diff --git a/q2_amr/card/tests/data/collated/card_gene_annotation/sample2/gene_mapping_data.txt b/q2_rgi/card/tests/data/collated/card_gene_annotation/sample2/gene_mapping_data.txt similarity index 100% rename from q2_amr/card/tests/data/collated/card_gene_annotation/sample2/gene_mapping_data.txt rename to q2_rgi/card/tests/data/collated/card_gene_annotation/sample2/gene_mapping_data.txt diff --git a/q2_amr/card/tests/data/kmer_json_test.json b/q2_rgi/card/tests/data/kmer_json_test.json similarity index 100% rename from q2_amr/card/tests/data/kmer_json_test.json rename to q2_rgi/card/tests/data/kmer_json_test.json diff --git a/q2_amr/card/tests/data/kmer_txt_test.txt b/q2_rgi/card/tests/data/kmer_txt_test.txt similarity index 100% rename from q2_amr/card/tests/data/kmer_txt_test.txt rename to q2_rgi/card/tests/data/kmer_txt_test.txt diff --git a/q2_amr/card/tests/data/output.allele_mapping_data.txt b/q2_rgi/card/tests/data/output.allele_mapping_data.txt similarity index 100% rename from q2_amr/card/tests/data/output.allele_mapping_data.txt rename to q2_rgi/card/tests/data/output.allele_mapping_data.txt diff --git a/q2_amr/card/tests/data/output.gene_mapping_data.txt b/q2_rgi/card/tests/data/output.gene_mapping_data.txt similarity index 100% rename from q2_amr/card/tests/data/output.gene_mapping_data.txt rename to q2_rgi/card/tests/data/output.gene_mapping_data.txt diff --git a/q2_amr/card/tests/data/output.mags.txt b/q2_rgi/card/tests/data/output.mags.txt similarity index 100% rename from q2_amr/card/tests/data/output.mags.txt rename to q2_rgi/card/tests/data/output.mags.txt diff --git a/q2_amr/card/tests/data/output.overall_mapping_stats.txt b/q2_rgi/card/tests/data/output.overall_mapping_stats.txt similarity index 100% rename from q2_amr/card/tests/data/output.overall_mapping_stats.txt rename to q2_rgi/card/tests/data/output.overall_mapping_stats.txt diff --git a/q2_amr/card/tests/data/output.sorted.length_100.bam b/q2_rgi/card/tests/data/output.sorted.length_100.bam similarity index 100% rename from q2_amr/card/tests/data/output.sorted.length_100.bam rename to q2_rgi/card/tests/data/output.sorted.length_100.bam diff --git a/q2_amr/card/tests/data/partitioned/annotate_mags_output_1/sample1/bin1/amr_annotation.json b/q2_rgi/card/tests/data/partitioned/annotate_mags_output_1/sample1/bin1/amr_annotation.json similarity index 100% rename from q2_amr/card/tests/data/partitioned/annotate_mags_output_1/sample1/bin1/amr_annotation.json rename to q2_rgi/card/tests/data/partitioned/annotate_mags_output_1/sample1/bin1/amr_annotation.json diff --git a/q2_amr/card/tests/data/partitioned/annotate_mags_output_1/sample1/bin1/amr_annotation.txt b/q2_rgi/card/tests/data/partitioned/annotate_mags_output_1/sample1/bin1/amr_annotation.txt similarity index 100% rename from q2_amr/card/tests/data/partitioned/annotate_mags_output_1/sample1/bin1/amr_annotation.txt rename to q2_rgi/card/tests/data/partitioned/annotate_mags_output_1/sample1/bin1/amr_annotation.txt diff --git a/q2_amr/card/tests/data/partitioned/annotate_mags_output_2/sample2/bin1/amr_annotation.json b/q2_rgi/card/tests/data/partitioned/annotate_mags_output_2/sample2/bin1/amr_annotation.json similarity index 100% rename from q2_amr/card/tests/data/partitioned/annotate_mags_output_2/sample2/bin1/amr_annotation.json rename to q2_rgi/card/tests/data/partitioned/annotate_mags_output_2/sample2/bin1/amr_annotation.json diff --git a/q2_amr/card/tests/data/partitioned/annotate_mags_output_2/sample2/bin1/amr_annotation.txt b/q2_rgi/card/tests/data/partitioned/annotate_mags_output_2/sample2/bin1/amr_annotation.txt similarity index 100% rename from q2_amr/card/tests/data/partitioned/annotate_mags_output_2/sample2/bin1/amr_annotation.txt rename to q2_rgi/card/tests/data/partitioned/annotate_mags_output_2/sample2/bin1/amr_annotation.txt diff --git a/q2_amr/card/tests/data/partitioned/annotate_mags_output_2/sample2/bin2/amr_annotation.json b/q2_rgi/card/tests/data/partitioned/annotate_mags_output_2/sample2/bin2/amr_annotation.json similarity index 100% rename from q2_amr/card/tests/data/partitioned/annotate_mags_output_2/sample2/bin2/amr_annotation.json rename to q2_rgi/card/tests/data/partitioned/annotate_mags_output_2/sample2/bin2/amr_annotation.json diff --git a/q2_amr/card/tests/data/partitioned/annotate_mags_output_2/sample2/bin2/amr_annotation.txt b/q2_rgi/card/tests/data/partitioned/annotate_mags_output_2/sample2/bin2/amr_annotation.txt similarity index 100% rename from q2_amr/card/tests/data/partitioned/annotate_mags_output_2/sample2/bin2/amr_annotation.txt rename to q2_rgi/card/tests/data/partitioned/annotate_mags_output_2/sample2/bin2/amr_annotation.txt diff --git a/q2_amr/card/tests/data/partitioned/annotate_reads_allele_output_1/sample1/allele_mapping_data.txt b/q2_rgi/card/tests/data/partitioned/annotate_reads_allele_output_1/sample1/allele_mapping_data.txt similarity index 100% rename from q2_amr/card/tests/data/partitioned/annotate_reads_allele_output_1/sample1/allele_mapping_data.txt rename to q2_rgi/card/tests/data/partitioned/annotate_reads_allele_output_1/sample1/allele_mapping_data.txt diff --git a/q2_amr/card/tests/data/partitioned/annotate_reads_allele_output_1/sample1/overall_mapping_stats.txt b/q2_rgi/card/tests/data/partitioned/annotate_reads_allele_output_1/sample1/overall_mapping_stats.txt similarity index 100% rename from q2_amr/card/tests/data/partitioned/annotate_reads_allele_output_1/sample1/overall_mapping_stats.txt rename to q2_rgi/card/tests/data/partitioned/annotate_reads_allele_output_1/sample1/overall_mapping_stats.txt diff --git a/q2_amr/card/tests/data/partitioned/annotate_reads_allele_output_1/sample1/sorted.length_100.bam b/q2_rgi/card/tests/data/partitioned/annotate_reads_allele_output_1/sample1/sorted.length_100.bam similarity index 100% rename from q2_amr/card/tests/data/partitioned/annotate_reads_allele_output_1/sample1/sorted.length_100.bam rename to q2_rgi/card/tests/data/partitioned/annotate_reads_allele_output_1/sample1/sorted.length_100.bam diff --git a/q2_amr/card/tests/data/partitioned/annotate_reads_allele_output_2/sample2/allele_mapping_data.txt b/q2_rgi/card/tests/data/partitioned/annotate_reads_allele_output_2/sample2/allele_mapping_data.txt similarity index 100% rename from q2_amr/card/tests/data/partitioned/annotate_reads_allele_output_2/sample2/allele_mapping_data.txt rename to q2_rgi/card/tests/data/partitioned/annotate_reads_allele_output_2/sample2/allele_mapping_data.txt diff --git a/q2_amr/card/tests/data/partitioned/annotate_reads_allele_output_2/sample2/overall_mapping_stats.txt b/q2_rgi/card/tests/data/partitioned/annotate_reads_allele_output_2/sample2/overall_mapping_stats.txt similarity index 100% rename from q2_amr/card/tests/data/partitioned/annotate_reads_allele_output_2/sample2/overall_mapping_stats.txt rename to q2_rgi/card/tests/data/partitioned/annotate_reads_allele_output_2/sample2/overall_mapping_stats.txt diff --git a/q2_amr/card/tests/data/partitioned/annotate_reads_allele_output_2/sample2/sorted.length_100.bam b/q2_rgi/card/tests/data/partitioned/annotate_reads_allele_output_2/sample2/sorted.length_100.bam similarity index 100% rename from q2_amr/card/tests/data/partitioned/annotate_reads_allele_output_2/sample2/sorted.length_100.bam rename to q2_rgi/card/tests/data/partitioned/annotate_reads_allele_output_2/sample2/sorted.length_100.bam diff --git a/q2_amr/card/tests/data/partitioned/annotate_reads_gene_output_1/sample1/gene_mapping_data.txt b/q2_rgi/card/tests/data/partitioned/annotate_reads_gene_output_1/sample1/gene_mapping_data.txt similarity index 100% rename from q2_amr/card/tests/data/partitioned/annotate_reads_gene_output_1/sample1/gene_mapping_data.txt rename to q2_rgi/card/tests/data/partitioned/annotate_reads_gene_output_1/sample1/gene_mapping_data.txt diff --git a/q2_amr/card/tests/data/partitioned/annotate_reads_gene_output_2/sample2/gene_mapping_data.txt b/q2_rgi/card/tests/data/partitioned/annotate_reads_gene_output_2/sample2/gene_mapping_data.txt similarity index 100% rename from q2_amr/card/tests/data/partitioned/annotate_reads_gene_output_2/sample2/gene_mapping_data.txt rename to q2_rgi/card/tests/data/partitioned/annotate_reads_gene_output_2/sample2/gene_mapping_data.txt diff --git a/q2_amr/card/tests/data/partitioned/kmer_analysis_mags_1/sample1/bin1/61mer_analysis.json b/q2_rgi/card/tests/data/partitioned/kmer_analysis_mags_1/sample1/bin1/61mer_analysis.json similarity index 100% rename from q2_amr/card/tests/data/partitioned/kmer_analysis_mags_1/sample1/bin1/61mer_analysis.json rename to q2_rgi/card/tests/data/partitioned/kmer_analysis_mags_1/sample1/bin1/61mer_analysis.json diff --git a/q2_amr/card/tests/data/partitioned/kmer_analysis_mags_1/sample1/bin1/61mer_analysis_rgi_summary.txt b/q2_rgi/card/tests/data/partitioned/kmer_analysis_mags_1/sample1/bin1/61mer_analysis_rgi_summary.txt similarity index 100% rename from q2_amr/card/tests/data/partitioned/kmer_analysis_mags_1/sample1/bin1/61mer_analysis_rgi_summary.txt rename to q2_rgi/card/tests/data/partitioned/kmer_analysis_mags_1/sample1/bin1/61mer_analysis_rgi_summary.txt diff --git a/q2_amr/card/tests/data/partitioned/kmer_analysis_mags_2/sample2/bin1/61mer_analysis.json b/q2_rgi/card/tests/data/partitioned/kmer_analysis_mags_2/sample2/bin1/61mer_analysis.json similarity index 100% rename from q2_amr/card/tests/data/partitioned/kmer_analysis_mags_2/sample2/bin1/61mer_analysis.json rename to q2_rgi/card/tests/data/partitioned/kmer_analysis_mags_2/sample2/bin1/61mer_analysis.json diff --git a/q2_amr/card/tests/data/partitioned/kmer_analysis_mags_2/sample2/bin1/61mer_analysis_rgi_summary.txt b/q2_rgi/card/tests/data/partitioned/kmer_analysis_mags_2/sample2/bin1/61mer_analysis_rgi_summary.txt similarity index 100% rename from q2_amr/card/tests/data/partitioned/kmer_analysis_mags_2/sample2/bin1/61mer_analysis_rgi_summary.txt rename to q2_rgi/card/tests/data/partitioned/kmer_analysis_mags_2/sample2/bin1/61mer_analysis_rgi_summary.txt diff --git a/q2_amr/card/tests/data/partitioned/kmer_analysis_mags_2/sample2/bin2/61mer_analysis.json b/q2_rgi/card/tests/data/partitioned/kmer_analysis_mags_2/sample2/bin2/61mer_analysis.json similarity index 100% rename from q2_amr/card/tests/data/partitioned/kmer_analysis_mags_2/sample2/bin2/61mer_analysis.json rename to q2_rgi/card/tests/data/partitioned/kmer_analysis_mags_2/sample2/bin2/61mer_analysis.json diff --git a/q2_amr/card/tests/data/partitioned/kmer_analysis_mags_2/sample2/bin2/61mer_analysis_rgi_summary.txt b/q2_rgi/card/tests/data/partitioned/kmer_analysis_mags_2/sample2/bin2/61mer_analysis_rgi_summary.txt similarity index 100% rename from q2_amr/card/tests/data/partitioned/kmer_analysis_mags_2/sample2/bin2/61mer_analysis_rgi_summary.txt rename to q2_rgi/card/tests/data/partitioned/kmer_analysis_mags_2/sample2/bin2/61mer_analysis_rgi_summary.txt diff --git a/q2_amr/card/tests/data/partitioned/kmer_analysis_reads_allele_1/sample1/61mer_analysis.allele.txt b/q2_rgi/card/tests/data/partitioned/kmer_analysis_reads_allele_1/sample1/61mer_analysis.allele.txt similarity index 100% rename from q2_amr/card/tests/data/partitioned/kmer_analysis_reads_allele_1/sample1/61mer_analysis.allele.txt rename to q2_rgi/card/tests/data/partitioned/kmer_analysis_reads_allele_1/sample1/61mer_analysis.allele.txt diff --git a/q2_amr/card/tests/data/partitioned/kmer_analysis_reads_allele_1/sample1/61mer_analysis.json b/q2_rgi/card/tests/data/partitioned/kmer_analysis_reads_allele_1/sample1/61mer_analysis.json similarity index 100% rename from q2_amr/card/tests/data/partitioned/kmer_analysis_reads_allele_1/sample1/61mer_analysis.json rename to q2_rgi/card/tests/data/partitioned/kmer_analysis_reads_allele_1/sample1/61mer_analysis.json diff --git a/q2_amr/card/tests/data/partitioned/kmer_analysis_reads_allele_2/sample2/61mer_analysis.allele.txt b/q2_rgi/card/tests/data/partitioned/kmer_analysis_reads_allele_2/sample2/61mer_analysis.allele.txt similarity index 100% rename from q2_amr/card/tests/data/partitioned/kmer_analysis_reads_allele_2/sample2/61mer_analysis.allele.txt rename to q2_rgi/card/tests/data/partitioned/kmer_analysis_reads_allele_2/sample2/61mer_analysis.allele.txt diff --git a/q2_amr/card/tests/data/partitioned/kmer_analysis_reads_allele_2/sample2/61mer_analysis.json b/q2_rgi/card/tests/data/partitioned/kmer_analysis_reads_allele_2/sample2/61mer_analysis.json similarity index 100% rename from q2_amr/card/tests/data/partitioned/kmer_analysis_reads_allele_2/sample2/61mer_analysis.json rename to q2_rgi/card/tests/data/partitioned/kmer_analysis_reads_allele_2/sample2/61mer_analysis.json diff --git a/q2_amr/card/tests/data/partitioned/kmer_analysis_reads_gene_1/sample1/61mer_analysis.gene.txt b/q2_rgi/card/tests/data/partitioned/kmer_analysis_reads_gene_1/sample1/61mer_analysis.gene.txt similarity index 100% rename from q2_amr/card/tests/data/partitioned/kmer_analysis_reads_gene_1/sample1/61mer_analysis.gene.txt rename to q2_rgi/card/tests/data/partitioned/kmer_analysis_reads_gene_1/sample1/61mer_analysis.gene.txt diff --git a/q2_amr/card/tests/data/partitioned/kmer_analysis_reads_gene_1/sample1/61mer_analysis.json b/q2_rgi/card/tests/data/partitioned/kmer_analysis_reads_gene_1/sample1/61mer_analysis.json similarity index 100% rename from q2_amr/card/tests/data/partitioned/kmer_analysis_reads_gene_1/sample1/61mer_analysis.json rename to q2_rgi/card/tests/data/partitioned/kmer_analysis_reads_gene_1/sample1/61mer_analysis.json diff --git a/q2_amr/card/tests/data/partitioned/kmer_analysis_reads_gene_2/sample2/61mer_analysis.gene.txt b/q2_rgi/card/tests/data/partitioned/kmer_analysis_reads_gene_2/sample2/61mer_analysis.gene.txt similarity index 100% rename from q2_amr/card/tests/data/partitioned/kmer_analysis_reads_gene_2/sample2/61mer_analysis.gene.txt rename to q2_rgi/card/tests/data/partitioned/kmer_analysis_reads_gene_2/sample2/61mer_analysis.gene.txt diff --git a/q2_amr/card/tests/data/partitioned/kmer_analysis_reads_gene_2/sample2/61mer_analysis.json b/q2_rgi/card/tests/data/partitioned/kmer_analysis_reads_gene_2/sample2/61mer_analysis.json similarity index 100% rename from q2_amr/card/tests/data/partitioned/kmer_analysis_reads_gene_2/sample2/61mer_analysis.json rename to q2_rgi/card/tests/data/partitioned/kmer_analysis_reads_gene_2/sample2/61mer_analysis.json diff --git a/q2_amr/card/tests/data/reads_paired/MANIFEST b/q2_rgi/card/tests/data/reads_paired/MANIFEST similarity index 100% rename from q2_amr/card/tests/data/reads_paired/MANIFEST rename to q2_rgi/card/tests/data/reads_paired/MANIFEST diff --git a/q2_amr/card/tests/data/reads_paired/metadata.yml b/q2_rgi/card/tests/data/reads_paired/metadata.yml similarity index 100% rename from q2_amr/card/tests/data/reads_paired/metadata.yml rename to q2_rgi/card/tests/data/reads_paired/metadata.yml diff --git a/q2_amr/card/tests/data/reads_paired/sample1_00_L001_R1_001.fastq.gz b/q2_rgi/card/tests/data/reads_paired/sample1_00_L001_R1_001.fastq.gz similarity index 100% rename from q2_amr/card/tests/data/reads_paired/sample1_00_L001_R1_001.fastq.gz rename to q2_rgi/card/tests/data/reads_paired/sample1_00_L001_R1_001.fastq.gz diff --git a/q2_amr/card/tests/data/reads_paired/sample1_00_L001_R2_001.fastq.gz b/q2_rgi/card/tests/data/reads_paired/sample1_00_L001_R2_001.fastq.gz similarity index 100% rename from q2_amr/card/tests/data/reads_paired/sample1_00_L001_R2_001.fastq.gz rename to q2_rgi/card/tests/data/reads_paired/sample1_00_L001_R2_001.fastq.gz diff --git a/q2_amr/card/tests/data/reads_single/MANIFEST b/q2_rgi/card/tests/data/reads_single/MANIFEST similarity index 100% rename from q2_amr/card/tests/data/reads_single/MANIFEST rename to q2_rgi/card/tests/data/reads_single/MANIFEST diff --git a/q2_amr/card/tests/data/reads_single/metadata.yml b/q2_rgi/card/tests/data/reads_single/metadata.yml similarity index 100% rename from q2_amr/card/tests/data/reads_single/metadata.yml rename to q2_rgi/card/tests/data/reads_single/metadata.yml diff --git a/q2_amr/card/tests/data/reads_single/sample1_00_L001_R1_001.fastq.gz b/q2_rgi/card/tests/data/reads_single/sample1_00_L001_R1_001.fastq.gz similarity index 100% rename from q2_amr/card/tests/data/reads_single/sample1_00_L001_R1_001.fastq.gz rename to q2_rgi/card/tests/data/reads_single/sample1_00_L001_R1_001.fastq.gz diff --git a/q2_amr/card/tests/data/rgi_output.json b/q2_rgi/card/tests/data/rgi_output.json similarity index 100% rename from q2_amr/card/tests/data/rgi_output.json rename to q2_rgi/card/tests/data/rgi_output.json diff --git a/q2_amr/card/tests/data/rgi_output.txt b/q2_rgi/card/tests/data/rgi_output.txt similarity index 100% rename from q2_amr/card/tests/data/rgi_output.txt rename to q2_rgi/card/tests/data/rgi_output.txt diff --git a/q2_amr/card/tests/data/wildcard_data.tar.bz2 b/q2_rgi/card/tests/data/wildcard_data.tar.bz2 similarity index 100% rename from q2_amr/card/tests/data/wildcard_data.tar.bz2 rename to q2_rgi/card/tests/data/wildcard_data.tar.bz2 diff --git a/q2_amr/card/tests/test_database.py b/q2_rgi/card/tests/test_database.py similarity index 90% rename from q2_amr/card/tests/test_database.py rename to q2_rgi/card/tests/test_database.py index 0f5ac2e..fd37876 100644 --- a/q2_amr/card/tests/test_database.py +++ b/q2_rgi/card/tests/test_database.py @@ -7,12 +7,12 @@ import requests from qiime2.plugin.testing import TestPluginBase -from q2_amr.card.database import download_with_progress_bar, fetch_card_db, preprocess -from q2_amr.types import CARDDatabaseDirectoryFormat, CARDKmerDatabaseDirectoryFormat +from q2_rgi.card.database import download_with_progress_bar, fetch_card_db, preprocess +from q2_rgi.types import CARDDatabaseDirectoryFormat, CARDKmerDatabaseDirectoryFormat class TestAnnotateMagsCard(TestPluginBase): - package = "q2_amr.card.tests" + package = "q2_rgi.card.tests" def mock_preprocess(self, dir, operation): if operation == "card": @@ -36,8 +36,8 @@ def test_fetch_card_db(self): wildcard_tar = self.get_data_path("wildcard_data.tar.bz2") # Patch requests.get, - with patch("q2_amr.card.database.download_with_progress_bar"), patch( - "q2_amr.card.database.preprocess", side_effect=self.mock_preprocess + with patch("q2_rgi.card.database.download_with_progress_bar"), patch( + "q2_rgi.card.database.preprocess", side_effect=self.mock_preprocess ), patch( "tarfile.open", side_effect=[tarfile.open(card_tar), tarfile.open(wildcard_tar)], @@ -74,7 +74,7 @@ def test_fetch_card_db(self): def test_connection_error(self): # Simulate a ConnectionError during requests.get with patch( - "q2_amr.card.database.download_with_progress_bar", + "q2_rgi.card.database.download_with_progress_bar", side_effect=requests.ConnectionError, ), self.assertRaisesRegex( requests.ConnectionError, @@ -85,14 +85,14 @@ def test_connection_error(self): def test_tarfile_read_error(self): # Simulate a tarfile.ReadError during tarfile.open with patch("tarfile.open", side_effect=tarfile.ReadError), patch( - "q2_amr.card.database.download_with_progress_bar" + "q2_rgi.card.database.download_with_progress_bar" ), self.assertRaisesRegex(tarfile.ReadError, "Tarfile is invalid."): fetch_card_db() def test_subprocess_error(self): # Simulate a subprocess.CalledProcessError during run_command with patch( - "q2_amr.card.database.run_command", + "q2_rgi.card.database.run_command", side_effect=subprocess.CalledProcessError(1, "cmd"), ), self.assertRaisesRegex( Exception, @@ -104,7 +104,7 @@ def test_subprocess_error(self): def test_preprocess_card(self): # Ensure preprocess calls run_command with the correct arguments for "card" # operation - with patch("q2_amr.card.database.run_command") as mock_run_command: + with patch("q2_rgi.card.database.run_command") as mock_run_command: preprocess("path_tmp", "card") mock_run_command.assert_called_once_with( ["rgi", "card_annotation", "-i", "card/card.json"], @@ -115,7 +115,7 @@ def test_preprocess_card(self): def test_preprocess_wildcard(self): # Ensure preprocess calls run_command with the correct arguments for "wildcard" # operation - with patch("q2_amr.card.database.run_command") as mock_run_command: + with patch("q2_rgi.card.database.run_command") as mock_run_command: preprocess("path_tmp", "wildcard") mock_run_command.assert_called_once_with( [ @@ -138,7 +138,7 @@ def test_download_with_progressbar(self): tar_path = "/path/to/downloaded/file.tar" with patch("requests.get") as mock_get, patch( - "q2_amr.card.database.tqdm" + "q2_rgi.card.database.tqdm" ) as mock_tqdm, patch("builtins.open") as mock_open: # Mock response object response_mock = MagicMock() diff --git a/q2_amr/card/tests/test_heatmap.py b/q2_rgi/card/tests/test_heatmap.py similarity index 88% rename from q2_amr/card/tests/test_heatmap.py rename to q2_rgi/card/tests/test_heatmap.py index d7664b4..9907dbb 100644 --- a/q2_amr/card/tests/test_heatmap.py +++ b/q2_rgi/card/tests/test_heatmap.py @@ -4,17 +4,17 @@ from qiime2.plugin.testing import TestPluginBase -from q2_amr.card.heatmap import ( +from q2_rgi.card.heatmap import ( InvalidParameterCombinationError, change_names, heatmap, run_rgi_heatmap, ) -from q2_amr.types import CARDAnnotationDirectoryFormat +from q2_rgi.types import CARDAnnotationDirectoryFormat class TestHeatmap(TestPluginBase): - package = "q2_amr.card.tests" + package = "q2_rgi.card.tests" def test_heatmap(self): amr_annotation = CARDAnnotationDirectoryFormat() @@ -28,7 +28,7 @@ def mock_run_rgi_heatmap(tmp, json_files_dir, clus, cat, display, frequency): file.write(file_type) with patch( - "q2_amr.card.heatmap.run_rgi_heatmap", side_effect=mock_run_rgi_heatmap + "q2_rgi.card.heatmap.run_rgi_heatmap", side_effect=mock_run_rgi_heatmap ), tempfile.TemporaryDirectory() as tmp: os.makedirs(os.path.join(tmp, "results")) heatmap(tmp, amr_annotation) @@ -45,7 +45,7 @@ def mock_run_rgi_heatmap(tmp, json_files_dir, clus, cat, display, frequency): self.assertTrue(os.path.exists(os.path.join(tmp, "q2templateassets"))) def test_run_rgi_heatmap(self): - with patch("q2_amr.card.heatmap.run_command") as mock_run_command: + with patch("q2_rgi.card.heatmap.run_command") as mock_run_command: run_rgi_heatmap( "path_tmp", "json_files_dir_path", "samples", "drug_class", "fill", True ) @@ -71,9 +71,9 @@ def test_run_rgi_heatmap(self): def test_change_names(self): with patch( - "q2_amr.card.heatmap.os.listdir", + "q2_rgi.card.heatmap.os.listdir", return_value=["heatmap-7.eps", "heatmap-7.png", "heatmap-7.csv"], - ), patch("q2_amr.card.heatmap.os.rename") as mock_rename: + ), patch("q2_rgi.card.heatmap.os.rename") as mock_rename: results_dir = "/path/to/results" change_names(results_dir) expected_calls = [ @@ -85,8 +85,8 @@ def test_change_names(self): self.assertEqual(expected_calls, actual_calls) def test_change_names_empty(self): - with patch("q2_amr.card.heatmap.os.listdir", return_value=[]), patch( - "q2_amr.card.heatmap.os.rename" + with patch("q2_rgi.card.heatmap.os.listdir", return_value=[]), patch( + "q2_rgi.card.heatmap.os.rename" ) as mock_rename: results_dir = "/path/to/results" change_names(results_dir) diff --git a/q2_amr/card/tests/test_kmer.py b/q2_rgi/card/tests/test_kmer.py similarity index 94% rename from q2_amr/card/tests/test_kmer.py rename to q2_rgi/card/tests/test_kmer.py index 2d40546..3e3c2a0 100644 --- a/q2_amr/card/tests/test_kmer.py +++ b/q2_rgi/card/tests/test_kmer.py @@ -6,7 +6,7 @@ import pytest from qiime2.plugin.testing import TestPluginBase -from q2_amr.card.kmer import ( +from q2_rgi.card.kmer import ( _kmer_query_mags, _kmer_query_reads, _run_rgi_kmer_query, @@ -15,7 +15,7 @@ kmer_query_reads_card, run_rgi_kmer_build, ) -from q2_amr.types import ( +from q2_rgi.types import ( CARDAlleleAnnotationDirectoryFormat, CARDAnnotationDirectoryFormat, CARDDatabaseDirectoryFormat, @@ -27,7 +27,7 @@ class TestKmer(TestPluginBase): - package = "q2_amr.card.tests" + package = "q2_rgi.card.tests" @classmethod def setUpClass(cls): @@ -81,8 +81,8 @@ def _run_kmer_query_test(self, annotation_format, output_format, query_function) # Patch _run_rgi_kmer_query and load_card_db functions with pytest.warns(UserWarning, match=warning), patch( - "q2_amr.card.kmer._run_rgi_kmer_query", side_effect=mock_run_rgi_kmer_query - ), patch("q2_amr.card.kmer.load_card_db", return_value="61"): + "q2_rgi.card.kmer._run_rgi_kmer_query", side_effect=mock_run_rgi_kmer_query + ), patch("q2_rgi.card.kmer.load_card_db", return_value="61"): # Run _kmer_query_reads or _kmer_query_mags result = query_function(card_db, kmer_db, amr_annotations) @@ -126,7 +126,7 @@ def test__kmer_query_reads_card(self): ) def test__run_rgi_kmer_query(self): - with patch("q2_amr.card.kmer.run_command") as mock_run_command: + with patch("q2_rgi.card.kmer.run_command") as mock_run_command: _run_rgi_kmer_query( tmp="path_tmp", input_file="path_input_file", @@ -217,7 +217,7 @@ def test_exception_raised(self): "An error was encountered while running rgi, " "(return code 1), please inspect stdout and stderr to learn more." ) - with patch("q2_amr.card.kmer.run_command") as mock_run_command: + with patch("q2_rgi.card.kmer.run_command") as mock_run_command: mock_run_command.side_effect = subprocess.CalledProcessError(1, "cmd") with self.assertRaises(Exception) as cm: _run_rgi_kmer_query( @@ -228,8 +228,8 @@ def test_exception_raised(self): def test_kmer_build_card(self): mock_run_rgi_kmer_build = MagicMock(side_effect=self.copy_kmer_build_files) with patch( - "q2_amr.card.kmer.run_rgi_kmer_build", side_effect=mock_run_rgi_kmer_build - ), patch("q2_amr.card.kmer.load_card_db"), patch("glob.glob"): + "q2_rgi.card.kmer.run_rgi_kmer_build", side_effect=mock_run_rgi_kmer_build + ), patch("q2_rgi.card.kmer.load_card_db"), patch("glob.glob"): card_db = CARDDatabaseDirectoryFormat() result = kmer_build_card(card_db=card_db, kmer_size=32) @@ -248,7 +248,7 @@ def copy_kmer_build_files( shutil.copy(self.get_data_path(scr_file), os.path.join(tmp, des_file)) def test_run_rgi_kmer_build(self): - with patch("q2_amr.card.kmer.run_command") as mock_run_command: + with patch("q2_rgi.card.kmer.run_command") as mock_run_command: run_rgi_kmer_build( tmp="path_tmp", input_directory="path_directory", diff --git a/q2_amr/card/tests/test_mags.py b/q2_rgi/card/tests/test_mags.py similarity index 85% rename from q2_amr/card/tests/test_mags.py rename to q2_rgi/card/tests/test_mags.py index 11a286e..895c88a 100644 --- a/q2_amr/card/tests/test_mags.py +++ b/q2_rgi/card/tests/test_mags.py @@ -6,12 +6,12 @@ from q2_types.per_sample_sequences import MultiMAGSequencesDirFmt from qiime2.plugin.testing import TestPluginBase -from q2_amr.card.mags import annotate_mags_card, run_rgi_main -from q2_amr.types import CARDAnnotationDirectoryFormat, CARDDatabaseDirectoryFormat +from q2_rgi.card.mags import annotate_mags_card, run_rgi_main +from q2_rgi.types import CARDAnnotationDirectoryFormat, CARDDatabaseDirectoryFormat class TestAnnotateMagsCard(TestPluginBase): - package = "q2_amr.card.tests" + package = "q2_rgi.card.tests" def mock_run_rgi_main( self, @@ -38,11 +38,11 @@ def test_annotate_mags_card(self): mock_create_count_table = MagicMock() mock_read_in_txt = MagicMock() with patch( - "q2_amr.card.mags.run_rgi_main", side_effect=self.mock_run_rgi_main - ), patch("q2_amr.card.mags.load_card_db"), patch( - "q2_amr.card.mags.read_in_txt", mock_read_in_txt + "q2_rgi.card.mags.run_rgi_main", side_effect=self.mock_run_rgi_main + ), patch("q2_rgi.card.mags.load_card_db"), patch( + "q2_rgi.card.mags.read_in_txt", mock_read_in_txt ), patch( - "q2_amr.card.mags.create_count_table", mock_create_count_table + "q2_rgi.card.mags.create_count_table", mock_create_count_table ): result = annotate_mags_card(mag, card_db) self.assertIsInstance(result[0], CARDAnnotationDirectoryFormat) @@ -62,7 +62,7 @@ def test_annotate_mags_card(self): ) def test_run_rgi_main(self): - with patch("q2_amr.card.mags.run_command") as mock_run_command: + with patch("q2_rgi.card.mags.run_command") as mock_run_command: run_rgi_main("path_tmp", "path_input", "DIAMOND", True, True, True, True, 8) mock_run_command.assert_called_once_with( [ @@ -94,7 +94,7 @@ def test_exception_raised(self): ) tmp = "path/to/tmp" input_sequence = "path/to/input_sequence.fasta" - with patch("q2_amr.card.mags.run_command") as mock_run_command: + with patch("q2_rgi.card.mags.run_command") as mock_run_command: mock_run_command.side_effect = subprocess.CalledProcessError(1, "cmd") with self.assertRaises(Exception) as cm: run_rgi_main(tmp, input_sequence) diff --git a/q2_amr/card/tests/test_partition.py b/q2_rgi/card/tests/test_partition.py similarity index 99% rename from q2_amr/card/tests/test_partition.py rename to q2_rgi/card/tests/test_partition.py index b6e9b7d..d2bda2a 100644 --- a/q2_amr/card/tests/test_partition.py +++ b/q2_rgi/card/tests/test_partition.py @@ -2,7 +2,7 @@ from qiime2.plugin.testing import TestPluginBase -from q2_amr.card.partition import ( +from q2_rgi.card.partition import ( collate_mags_annotations, collate_mags_kmer_analyses, collate_reads_allele_annotations, @@ -13,7 +13,7 @@ partition_reads_allele_annotations, partition_reads_gene_annotations, ) -from q2_amr.types import ( +from q2_rgi.types import ( CARDAlleleAnnotationDirectoryFormat, CARDAnnotationDirectoryFormat, CARDGeneAnnotationDirectoryFormat, @@ -24,7 +24,7 @@ class TestPartition(TestPluginBase): - package = "q2_amr.card.tests" + package = "q2_rgi.card.tests" def test_collate_mags_annotations(self): # Test collate for mags annotations diff --git a/q2_amr/card/tests/test_reads.py b/q2_rgi/card/tests/test_reads.py similarity index 94% rename from q2_amr/card/tests/test_reads.py rename to q2_rgi/card/tests/test_reads.py index fa017bb..4ecd74b 100644 --- a/q2_amr/card/tests/test_reads.py +++ b/q2_rgi/card/tests/test_reads.py @@ -10,8 +10,8 @@ from qiime2 import Artifact from qiime2.plugin.testing import TestPluginBase -from q2_amr.card.reads import _annotate_reads_card, annotate_reads_card, run_rgi_bwt -from q2_amr.types import ( +from q2_rgi.card.reads import _annotate_reads_card, annotate_reads_card, run_rgi_bwt +from q2_rgi.types import ( CARDAlleleAnnotationDirectoryFormat, CARDDatabaseDirectoryFormat, CARDGeneAnnotationDirectoryFormat, @@ -19,7 +19,7 @@ class TestAnnotateReadsCARD(TestPluginBase): - package = "q2_amr.card.tests" + package = "q2_rgi.card.tests" @classmethod def setUpClass(cls): @@ -74,10 +74,10 @@ def annotate_reads_card_test_body(self, read_type): # Patch run_rgi_bwt, run_rgi_load, read_in_txt and create_count_table functions # and assign MagicMock objects - with patch("q2_amr.card.reads.run_rgi_bwt", mock_run_rgi_bwt), patch( - "q2_amr.card.reads.load_card_db", mock_run_rgi_load - ), patch("q2_amr.card.reads.read_in_txt", mock_read_in_txt), patch( - "q2_amr.card.reads.create_count_table", mock_create_count_table + with patch("q2_rgi.card.reads.run_rgi_bwt", mock_run_rgi_bwt), patch( + "q2_rgi.card.reads.load_card_db", mock_run_rgi_load + ), patch("q2_rgi.card.reads.read_in_txt", mock_read_in_txt), patch( + "q2_rgi.card.reads.create_count_table", mock_create_count_table ): # Run _annotate_reads_card function result = _annotate_reads_card(reads, card_db) @@ -153,7 +153,7 @@ def annotate_reads_card_test_body(self, read_type): ) def test_run_rgi_bwt(self): - with patch("q2_amr.card.reads.run_command") as mock_run_command: + with patch("q2_rgi.card.reads.run_command") as mock_run_command: run_rgi_bwt( "path_tmp", "sample1", @@ -193,7 +193,7 @@ def test_exception_raised(self): ) with patch( - "q2_amr.card.reads.run_command" + "q2_rgi.card.reads.run_command" ) as mock_run_command, self.assertRaises(Exception) as cm: mock_run_command.side_effect = subprocess.CalledProcessError(1, "cmd") run_rgi_bwt() diff --git a/q2_amr/card/tests/test_utils.py b/q2_rgi/card/tests/test_utils.py similarity index 97% rename from q2_amr/card/tests/test_utils.py rename to q2_rgi/card/tests/test_utils.py index d5eb6c1..a29e035 100644 --- a/q2_amr/card/tests/test_utils.py +++ b/q2_rgi/card/tests/test_utils.py @@ -6,18 +6,18 @@ import pandas as pd from qiime2.plugin.testing import TestPluginBase -from q2_amr.card.utils import ( +from q2_rgi.card.utils import ( colorify, copy_files, create_count_table, load_card_db, read_in_txt, ) -from q2_amr.types import CARDDatabaseDirectoryFormat, CARDKmerDatabaseDirectoryFormat +from q2_rgi.types import CARDDatabaseDirectoryFormat, CARDKmerDatabaseDirectoryFormat class TestAnnotateReadsCARD(TestPluginBase): - package = "q2_amr.card.tests" + package = "q2_rgi.card.tests" @classmethod def setUpClass(cls): @@ -76,7 +76,7 @@ def test_load_card_db_fasta(self): shutil.copy(self.get_data_path(src), os.path.join(str(dir), des)) # Patch run_command - with patch("q2_amr.card.utils.run_command") as mock_run_command: + with patch("q2_rgi.card.utils.run_command") as mock_run_command: # Run load_card_db two times with include_other_models set to True and False for parameters in [False, True]: kmer_size = load_card_db( @@ -135,7 +135,7 @@ def test_exception_raised(self): "(return code 1), please inspect stdout and stderr to learn more." ) with patch( - "q2_amr.card.utils.run_command" + "q2_rgi.card.utils.run_command" ) as mock_run_command, self.assertRaises(Exception) as cm: mock_run_command.side_effect = subprocess.CalledProcessError(1, "cmd") load_card_db() diff --git a/q2_amr/card/utils.py b/q2_rgi/card/utils.py similarity index 100% rename from q2_amr/card/utils.py rename to q2_rgi/card/utils.py diff --git a/q2_amr/citations.bib b/q2_rgi/citations.bib similarity index 100% rename from q2_amr/citations.bib rename to q2_rgi/citations.bib diff --git a/q2_amr/plugin_setup.py b/q2_rgi/plugin_setup.py similarity index 98% rename from q2_amr/plugin_setup.py rename to q2_rgi/plugin_setup.py index a508ff1..e330598 100644 --- a/q2_amr/plugin_setup.py +++ b/q2_rgi/plugin_setup.py @@ -27,18 +27,18 @@ ) from qiime2.plugin import Citations, Plugin -from q2_amr import __version__ -from q2_amr.card.database import fetch_card_db -from q2_amr.card.heatmap import heatmap -from q2_amr.card.kmer import ( +from q2_rgi import __version__ +from q2_rgi.card.database import fetch_card_db +from q2_rgi.card.heatmap import heatmap +from q2_rgi.card.kmer import ( _kmer_query_mags, _kmer_query_reads, kmer_build_card, kmer_query_mags_card, kmer_query_reads_card, ) -from q2_amr.card.mags import annotate_mags_card -from q2_amr.card.partition import ( +from q2_rgi.card.mags import annotate_mags_card +from q2_rgi.card.partition import ( collate_mags_annotations, collate_mags_kmer_analyses, collate_reads_allele_annotations, @@ -49,15 +49,15 @@ partition_reads_allele_annotations, partition_reads_gene_annotations, ) -from q2_amr.card.reads import _annotate_reads_card, annotate_reads_card -from q2_amr.types import ( +from q2_rgi.card.reads import _annotate_reads_card, annotate_reads_card +from q2_rgi.types import ( CARDAnnotationJSONFormat, CARDAnnotationTXTFormat, CARDDatabase, CARDDatabaseDirectoryFormat, CARDDatabaseFormat, ) -from q2_amr.types._format import ( +from q2_rgi.types._format import ( CARDAlleleAnnotationDirectoryFormat, CARDAlleleAnnotationFormat, CARDAnnotationDirectoryFormat, @@ -78,7 +78,7 @@ CARDWildcardIndexFormat, GapDNAFASTAFormat, ) -from q2_amr.types._type import ( +from q2_rgi.types._type import ( CARDAlleleAnnotation, CARDAnnotation, CARDGeneAnnotation, @@ -88,13 +88,13 @@ CARDReadsGeneKmerAnalysis, ) -citations = Citations.load("citations.bib", package="q2_amr") +citations = Citations.load("citations.bib", package="q2_rgi") plugin = Plugin( name="amr", version=__version__, - website="https://github.com/bokulich-lab/q2-amr", - package="q2_amr", + website="https://github.com/bokulich-lab/q2-rgi", + package="q2_rgi", description="This is a QIIME 2 plugin that annotates sequence data with " "antimicrobial resistance gene information from CARD.", short_description="This is a QIIME 2 plugin that annotates sequence " @@ -1133,4 +1133,4 @@ CARDReadsAlleleKmerAnalysisDirectoryFormat, ) -importlib.import_module("q2_amr.types._transformer") +importlib.import_module("q2_rgi.types._transformer") diff --git a/q2_amr/types/__init__.py b/q2_rgi/types/__init__.py similarity index 90% rename from q2_amr/types/__init__.py rename to q2_rgi/types/__init__.py index 2b015b1..025b08e 100644 --- a/q2_amr/types/__init__.py +++ b/q2_rgi/types/__init__.py @@ -1,11 +1,10 @@ # ---------------------------------------------------------------------------- -# Copyright (c) 2019-2023, QIIME 2 development team. +# Copyright (c) 2022, Bokulich Lab. # # Distributed under the terms of the Modified BSD License. # # The full license is in the file LICENSE, distributed with this software. # ---------------------------------------------------------------------------- - from ._format import ( CARDAlleleAnnotationDirectoryFormat, CARDAlleleAnnotationFormat, @@ -37,35 +36,41 @@ CARDDatabase, CARDGeneAnnotation, CARDKmerDatabase, + CARDMAGsKmerAnalysis, + CARDReadsAlleleKmerAnalysis, + CARDReadsGeneKmerAnalysis, ) __all__ = [ - "CARDDatabaseFormat", - "CARDDatabaseDirectoryFormat", + "CARDKmerDatabaseDirectoryFormat", + "CARDKmerJSONFormat", + "CARDKmerTXTFormat", + "CARDMAGsKmerAnalysisDirectoryFormat", + "GapDNAFASTAFormat", + "CARDWildcardIndexFormat", "CARDAnnotationTXTFormat", "CARDAnnotationJSONFormat", "CARDAnnotationDirectoryFormat", + "CARDDatabaseFormat", + "CARDDatabaseDirectoryFormat", "CARDAlleleAnnotationFormat", "CARDGeneAnnotationFormat", "CARDAnnotationStatsFormat", "CARDAlleleAnnotationDirectoryFormat", "CARDGeneAnnotationDirectoryFormat", - "CARDDatabase", - "CARDAnnotation", - "CARDAlleleAnnotation", - "CARDGeneAnnotation", - "CARDKmerDatabaseDirectoryFormat", - "CARDKmerJSONFormat", - "CARDKmerTXTFormat", - "GapDNAFASTAFormat", - "CARDWildcardIndexFormat", - "CARDKmerDatabase", "CARDMAGsKmerAnalysisFormat", "CARDMAGsKmerAnalysisJSONFormat", - "CARDMAGsKmerAnalysisDirectoryFormat", "CARDReadsAlleleKmerAnalysisFormat", "CARDReadsGeneKmerAnalysisFormat", "CARDReadsKmerAnalysisJSONFormat", "CARDReadsGeneKmerAnalysisDirectoryFormat", "CARDReadsAlleleKmerAnalysisDirectoryFormat", + "CARDDatabase", + "CARDKmerDatabase", + "CARDAnnotation", + "CARDAlleleAnnotation", + "CARDGeneAnnotation", + "CARDReadsGeneKmerAnalysis", + "CARDReadsAlleleKmerAnalysis", + "CARDMAGsKmerAnalysis", ] diff --git a/q2_amr/types/_format.py b/q2_rgi/types/_format.py similarity index 100% rename from q2_amr/types/_format.py rename to q2_rgi/types/_format.py diff --git a/q2_amr/types/_transformer.py b/q2_rgi/types/_transformer.py similarity index 99% rename from q2_amr/types/_transformer.py rename to q2_rgi/types/_transformer.py index 1139f7d..2c38d74 100644 --- a/q2_amr/types/_transformer.py +++ b/q2_rgi/types/_transformer.py @@ -18,7 +18,7 @@ from q2_types.genome_data import GenesDirectoryFormat, ProteinsDirectoryFormat from skbio import DNA, Protein -from q2_amr.types import CARDAnnotationDirectoryFormat +from q2_rgi.types import CARDAnnotationDirectoryFormat from ..plugin_setup import plugin from ._format import ( diff --git a/q2_amr/types/_type.py b/q2_rgi/types/_type.py similarity index 100% rename from q2_amr/types/_type.py rename to q2_rgi/types/_type.py diff --git a/q2_amr/types/tests/__init__.py b/q2_rgi/types/tests/__init__.py similarity index 100% rename from q2_amr/types/tests/__init__.py rename to q2_rgi/types/tests/__init__.py diff --git a/q2_amr/types/tests/data/61mer_analysis.allele.txt b/q2_rgi/types/tests/data/61mer_analysis.allele.txt similarity index 100% rename from q2_amr/types/tests/data/61mer_analysis.allele.txt rename to q2_rgi/types/tests/data/61mer_analysis.allele.txt diff --git a/q2_amr/types/tests/data/61mer_analysis.gene.txt b/q2_rgi/types/tests/data/61mer_analysis.gene.txt similarity index 100% rename from q2_amr/types/tests/data/61mer_analysis.gene.txt rename to q2_rgi/types/tests/data/61mer_analysis.gene.txt diff --git a/q2_amr/types/tests/data/61mer_analysis_rgi_summary.txt b/q2_rgi/types/tests/data/61mer_analysis_rgi_summary.txt similarity index 100% rename from q2_amr/types/tests/data/61mer_analysis_rgi_summary.txt rename to q2_rgi/types/tests/data/61mer_analysis_rgi_summary.txt diff --git a/q2_amr/types/tests/data/DNA_fasta.fasta b/q2_rgi/types/tests/data/DNA_fasta.fasta similarity index 100% rename from q2_amr/types/tests/data/DNA_fasta.fasta rename to q2_rgi/types/tests/data/DNA_fasta.fasta diff --git a/q2_amr/types/tests/data/DNA_fasta_-.fasta b/q2_rgi/types/tests/data/DNA_fasta_-.fasta similarity index 100% rename from q2_amr/types/tests/data/DNA_fasta_-.fasta rename to q2_rgi/types/tests/data/DNA_fasta_-.fasta diff --git a/q2_amr/types/tests/data/card_allele_annotation/sample1/allele_mapping_data.txt b/q2_rgi/types/tests/data/card_allele_annotation/sample1/allele_mapping_data.txt similarity index 100% rename from q2_amr/types/tests/data/card_allele_annotation/sample1/allele_mapping_data.txt rename to q2_rgi/types/tests/data/card_allele_annotation/sample1/allele_mapping_data.txt diff --git a/q2_amr/types/tests/data/card_allele_annotation/sample1/overall_mapping_stats.txt b/q2_rgi/types/tests/data/card_allele_annotation/sample1/overall_mapping_stats.txt similarity index 100% rename from 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b/q2_rgi/types/tests/data/kmer_json_test.json similarity index 100% rename from q2_amr/types/tests/data/kmer_json_test.json rename to q2_rgi/types/tests/data/kmer_json_test.json diff --git a/q2_amr/types/tests/data/kmer_txt_test.txt b/q2_rgi/types/tests/data/kmer_txt_test.txt similarity index 100% rename from q2_amr/types/tests/data/kmer_txt_test.txt rename to q2_rgi/types/tests/data/kmer_txt_test.txt diff --git a/q2_amr/types/tests/data/mags_61mer_analysis.json b/q2_rgi/types/tests/data/mags_61mer_analysis.json similarity index 100% rename from q2_amr/types/tests/data/mags_61mer_analysis.json rename to q2_rgi/types/tests/data/mags_61mer_analysis.json diff --git a/q2_amr/types/tests/data/reads_61mer_analysis.json b/q2_rgi/types/tests/data/reads_61mer_analysis.json similarity index 100% rename from q2_amr/types/tests/data/reads_61mer_analysis.json rename to q2_rgi/types/tests/data/reads_61mer_analysis.json diff --git a/q2_amr/types/tests/data/rgi_output.json b/q2_rgi/types/tests/data/rgi_output.json similarity index 100% rename from q2_amr/types/tests/data/rgi_output.json rename to q2_rgi/types/tests/data/rgi_output.json diff --git a/q2_amr/types/tests/data/rgi_output.txt b/q2_rgi/types/tests/data/rgi_output.txt similarity index 100% rename from q2_amr/types/tests/data/rgi_output.txt rename to q2_rgi/types/tests/data/rgi_output.txt diff --git a/q2_amr/types/tests/data/rgi_output_dna.fna b/q2_rgi/types/tests/data/rgi_output_dna.fna similarity index 100% rename from q2_amr/types/tests/data/rgi_output_dna.fna rename to q2_rgi/types/tests/data/rgi_output_dna.fna diff --git a/q2_amr/types/tests/data/rgi_output_protein.fna b/q2_rgi/types/tests/data/rgi_output_protein.fna similarity index 100% rename from q2_amr/types/tests/data/rgi_output_protein.fna rename to q2_rgi/types/tests/data/rgi_output_protein.fna diff --git a/q2_amr/types/tests/data/tabulated_df_allele.txt b/q2_rgi/types/tests/data/tabulated_df_allele.txt similarity index 100% rename from q2_amr/types/tests/data/tabulated_df_allele.txt rename to q2_rgi/types/tests/data/tabulated_df_allele.txt diff --git a/q2_amr/types/tests/data/tabulated_df_mags.txt b/q2_rgi/types/tests/data/tabulated_df_mags.txt similarity index 100% rename from q2_amr/types/tests/data/tabulated_df_mags.txt rename to q2_rgi/types/tests/data/tabulated_df_mags.txt diff --git a/q2_amr/types/tests/test_types_formats_transformers.py b/q2_rgi/types/tests/test_types_formats_transformers.py similarity index 98% rename from q2_amr/types/tests/test_types_formats_transformers.py rename to q2_rgi/types/tests/test_types_formats_transformers.py index a871e99..9908a9c 100644 --- a/q2_amr/types/tests/test_types_formats_transformers.py +++ b/q2_rgi/types/tests/test_types_formats_transformers.py @@ -24,12 +24,12 @@ from qiime2.plugin.testing import TestPluginBase from skbio import DNA, Protein -from q2_amr.types import ( +from q2_rgi.types import ( CARDAlleleAnnotationDirectoryFormat, CARDDatabaseDirectoryFormat, CARDGeneAnnotationDirectoryFormat, ) -from q2_amr.types._format import ( +from q2_rgi.types._format import ( CARDAnnotationDirectoryFormat, CARDAnnotationTXTFormat, CARDDatabaseFormat, @@ -47,7 +47,7 @@ CARDWildcardIndexFormat, GapDNAFASTAFormat, ) -from q2_amr.types._transformer import ( +from q2_rgi.types._transformer import ( _read_from_card_file, card_annotation_df_to_fasta, extract_sequence, @@ -56,11 +56,11 @@ class AMRTypesTestPluginBase(TestPluginBase): - package = "q2_amr.types.tests" + package = "q2_rgi.types.tests" def setUp(self): super().setUp() - self.temp_dir = tempfile.TemporaryDirectory(prefix="q2-amr-test-temp-") + self.temp_dir = tempfile.TemporaryDirectory(prefix="q2-rgi-test-temp-") def tearDown(self): self.temp_dir.cleanup() @@ -69,7 +69,9 @@ def get_data_path(self, filename): return pkg_resources.resource_filename(self.package, "data/%s" % filename) -class TestCARDDatabaseTypesAndFormats(AMRTypesTestPluginBase): +class TestCARDDatabaseTypesAndFormats(TestPluginBase): + package = "q2_rgi.types.tests" + def test_card_database_format_validate_positive(self): filepath = self.get_data_path("card_test.json") format = CARDDatabaseFormat(filepath, mode="r") diff --git a/setup.cfg b/setup.cfg index 8b510de..7ced596 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,10 +1,10 @@ [versioneer] VCS=git style=pep440 -versionfile_source = q2_amr/_version.py -versionfile_build = q2_amr/_version.py +versionfile_source = q2_rgi/_version.py +versionfile_build = q2_rgi/_version.py tag_prefix = -parentdir_prefix = q2-amr- +parentdir_prefix = q2-rgi- [flake8] max-line-length = 88 diff --git a/setup.py b/setup.py index a08c229..2ef7083 100644 --- a/setup.py +++ b/setup.py @@ -11,7 +11,7 @@ import versioneer setup( - name="q2-amr", + name="q2-rgi", version=versioneer.get_version(), cmdclass=versioneer.get_cmdclass(), license="BSD-3-Clause", @@ -20,20 +20,20 @@ author_email="risch.vinzent@gmail.com", description="This is a QIIME 2 plugin that annotates microbiome sequence data with " "antimicrobial resistance gene information from CARD.", - url="https://github.com/bokulich-lab/q2-amr", - entry_points={"qiime2.plugins": ["q2-amr=q2_amr.plugin_setup:plugin"]}, + url="https://github.com/bokulich-lab/q2-rgi", + entry_points={"qiime2.plugins": ["q2-rgi=q2_rgi.plugin_setup:plugin"]}, package_data={ - "q2_amr": [ + "q2_rgi": [ "citations.bib", "assets/rgi/annotation_stats/*", "assets/rgi/heatmap/*", ], - "q2_amr.types.tests": [ + "q2_rgi.types.tests": [ "data/*", "data/*/*/*", "data/*/*/*/*", ], - "q2_amr.card.tests": [ + "q2_rgi.card.tests": [ "data/*", "data/*/*", "data/*/*/*/*",