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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,129 @@ | ||
| from typing import Union | ||
|
|
||
| from q2_types.feature_data_mag import MAGSequencesDirFmt | ||
| from q2_types.genome_data import ( | ||
| GenesDirectoryFormat, | ||
| LociDirectoryFormat, | ||
| ProteinsDirectoryFormat, | ||
| ) | ||
| from q2_types.per_sample_sequences import ContigSequencesDirFmt, MultiMAGSequencesDirFmt | ||
|
|
||
| from q2_amrfinderplus.types import ( | ||
| AMRFinderPlusAnnotationsDirFmt, | ||
| AMRFinderPlusDatabaseDirFmt, | ||
| ) | ||
| from q2_amrfinderplus.utils import ( | ||
| _create_empty_files, | ||
| _create_sample_dict, | ||
| _create_sample_dirs, | ||
| _get_file_paths, | ||
| _run_amrfinderplus_analyse, | ||
| _validate_inputs, | ||
| ) | ||
|
|
||
|
|
||
| def annotate( | ||
| amrfinderplus_db: AMRFinderPlusDatabaseDirFmt, | ||
| sequences: Union[ | ||
| MultiMAGSequencesDirFmt, ContigSequencesDirFmt, MAGSequencesDirFmt | ||
| ] = None, | ||
| proteins: ProteinsDirectoryFormat = None, | ||
| loci: LociDirectoryFormat = None, | ||
| organism: str = None, | ||
| plus: bool = False, | ||
| report_all_equal: bool = False, | ||
| ident_min: float = None, | ||
| curated_ident: bool = False, | ||
| coverage_min: float = 0.5, | ||
| translation_table: str = "11", | ||
| annotation_format: str = "prodigal", | ||
| report_common: bool = False, | ||
| threads: int = None, | ||
| ) -> ( | ||
| AMRFinderPlusAnnotationsDirFmt, | ||
| AMRFinderPlusAnnotationsDirFmt, | ||
| GenesDirectoryFormat, | ||
| ProteinsDirectoryFormat, | ||
| ): | ||
| # Validate input and parameter combinations | ||
| _validate_inputs( | ||
| sequences, | ||
| loci, | ||
| proteins, | ||
| ident_min, | ||
| curated_ident, | ||
| report_common, | ||
| plus, | ||
| organism, | ||
| ) | ||
|
|
||
| # Set up common parameters for _run_amrfinderplus_analyse | ||
| common_params = locals().copy() | ||
| del common_params["sequences"] | ||
| del common_params["proteins"] | ||
| del common_params["loci"] | ||
|
|
||
| # Innit output formats | ||
| amr_annotations = AMRFinderPlusAnnotationsDirFmt() | ||
| amr_all_mutations = AMRFinderPlusAnnotationsDirFmt() | ||
| amr_genes = GenesDirectoryFormat() | ||
| amr_proteins = ProteinsDirectoryFormat() | ||
|
|
||
| # Create sample_dict to iterate over input files | ||
| sample_dict = _create_sample_dict(proteins, sequences) | ||
|
|
||
| # Iterate over sample_dict | ||
| for sample_id, files_dict in sample_dict.items(): | ||
| # Create sample directories in output directories | ||
| _create_sample_dirs( | ||
| sequences, | ||
| proteins, | ||
| organism, | ||
| amr_annotations, | ||
| amr_genes, | ||
| amr_proteins, | ||
| amr_all_mutations, | ||
| sample_id, | ||
| ) | ||
|
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||
| for id, file_fp in files_dict.items(): | ||
| # Construct and validate file input paths for amrfinderplus | ||
| dna_path, protein_path, gff_path = _get_file_paths( | ||
| sequences, | ||
| proteins, | ||
| loci, | ||
| id, | ||
| file_fp, | ||
| sample_id, | ||
| ) | ||
|
|
||
| # Define paths for output files | ||
| amr_annotations_path = ( | ||
| amr_annotations.path / sample_id / f"{id}_amr_annotations.tsv" | ||
| ) | ||
| amr_genes_path = amr_genes.path / sample_id / f"{id}_amr_genes.fasta" | ||
| amr_proteins_path = ( | ||
| amr_proteins.path / sample_id / f"{id}_amr_proteins.fasta" | ||
| ) | ||
| amr_all_mutations_path = ( | ||
| amr_all_mutations.path / sample_id / f"{id}_amr_all_mutations.tsv" | ||
| ) | ||
|
|
||
| # Run amrfinderplus | ||
| _run_amrfinderplus_analyse( | ||
| dna_path=dna_path, | ||
| protein_path=protein_path, | ||
| gff_path=gff_path, | ||
| amr_annotations_path=amr_annotations_path, | ||
| amr_genes_path=amr_genes_path, | ||
| amr_proteins_path=amr_proteins_path, | ||
| amr_all_mutations_path=amr_all_mutations_path, | ||
| **common_params, | ||
| ) | ||
|
|
||
| # Create empty files for empty output artifacts if needed | ||
| _create_empty_files( | ||
| sequences, proteins, organism, amr_genes, amr_proteins, amr_all_mutations | ||
| ) | ||
|
|
||
| return amr_annotations, amr_all_mutations, amr_genes, amr_proteins |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,47 @@ | ||
| from unittest.mock import patch | ||
|
|
||
| from q2_types.genome_data import GenesDirectoryFormat, ProteinsDirectoryFormat | ||
| from qiime2.plugin.testing import TestPluginBase | ||
|
|
||
| from q2_amrfinderplus.annotate import annotate | ||
| from q2_amrfinderplus.types import ( | ||
| AMRFinderPlusAnnotationsDirFmt, | ||
| AMRFinderPlusDatabaseDirFmt, | ||
| ) | ||
|
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||
|
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| class TestAnnotate(TestPluginBase): | ||
| package = "q2_amrfinderplus.tests" | ||
|
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||
| @patch("q2_amrfinderplus.annotate._validate_inputs") | ||
| @patch( | ||
| "q2_amrfinderplus.annotate._create_sample_dict", | ||
| return_value={"sample1": {"id1": "file_path"}}, | ||
| ) | ||
| @patch("q2_amrfinderplus.annotate._create_sample_dirs") | ||
| @patch( | ||
| "q2_amrfinderplus.annotate._get_file_paths", | ||
| return_value=("dna_path", "protein_path", "gff_path"), | ||
| ) | ||
| @patch("q2_amrfinderplus.annotate._run_amrfinderplus_analyse") | ||
| @patch("q2_amrfinderplus.annotate._create_empty_files") | ||
| def test_annotate( | ||
| self, | ||
| mock_create_empty_files, | ||
| mock_run_amrfinderplus, | ||
| mock_get_file_paths, | ||
| mock_create_sample_dirs, | ||
| mock_create_sample_dict, | ||
| mock_validate_inputs, | ||
| ): | ||
| # Create mock for the AMRFinderPlusDatabaseDirFmt input | ||
| amrfinderplus_db = AMRFinderPlusDatabaseDirFmt() | ||
|
|
||
| # Call the function with mostly default inputs | ||
| result = annotate(amrfinderplus_db) | ||
|
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| # Ensure the output is the correct types | ||
| self.assertIsInstance(result[0], AMRFinderPlusAnnotationsDirFmt) | ||
| self.assertIsInstance(result[1], AMRFinderPlusAnnotationsDirFmt) | ||
| self.assertIsInstance(result[2], GenesDirectoryFormat) | ||
| self.assertIsInstance(result[3], ProteinsDirectoryFormat) |
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