From 2127e9a7534cc10c4b1830fa748b3bca173d17c0 Mon Sep 17 00:00:00 2001 From: Marco van Zwetselaar Date: Mon, 30 Dec 2024 11:41:07 +0300 Subject: [PATCH] Remove pointfinder tests --- test/run_integration_test.sh | 3 --- test/test_parsing_validity.py | 26 -------------------------- 2 files changed, 29 deletions(-) diff --git a/test/run_integration_test.sh b/test/run_integration_test.sh index 64bdb11..6c863bd 100755 --- a/test/run_integration_test.sh +++ b/test/run_integration_test.sh @@ -27,9 +27,6 @@ hamronize rgi --input_file_name rgi_report --analysis_software_version rgi_v1 -- hamronize resfinder data/raw_outputs/resfinder/data_resfinder.json --format json --output hamronized_resfinder.json hamronize resfinder data/raw_outputs/resfinder/data_resfinder.json --format tsv --output hamronized_resfinder.tsv -hamronize pointfinder --input_file_name pointfinder_report --analysis_software_version resfinder_v4 --reference_database_version pointfinder_db_v1 data/raw_outputs/pointfinder/PointFinder_results.txt --format json --output hamronized_pointfinder.json -hamronize pointfinder --input_file_name pointfinder_report --analysis_software_version resfinder_v4 --reference_database_version pointfinder_db_v1 data/raw_outputs/pointfinder/PointFinder_results.txt --format tsv --output hamronized_pointfinder.tsv - hamronize srax --reference_database_name srax_default --input_file_name srax_report --reference_database_version srax_db_v1 --analysis_software_version srax_v1 --format json data/raw_outputs/srax/sraX_detected_ARGs.tsv --output hamronized_srax.json hamronize srax --reference_database_name srax_default --input_file_name srax_report --reference_database_version srax_db_v1 --analysis_software_version srax_v1 --format tsv data/raw_outputs/srax/sraX_detected_ARGs.tsv --output hamronized_srax.tsv diff --git a/test/test_parsing_validity.py b/test/test_parsing_validity.py index d098ff1..74c7cf2 100644 --- a/test/test_parsing_validity.py +++ b/test/test_parsing_validity.py @@ -292,32 +292,6 @@ def test_kmerresistance(): assert result.reference_gene_stop is None -def test_pointfinder(): - metadata = { - "analysis_software_version": "4.1.0", - "reference_database_version": "2021-02-01", - "input_file_name": "Dummy", - } - parsed_report = hAMRonization.parse( - "data/dummy/pointfinder/PointFinder_results.txt", metadata, "pointfinder" - ) - - for result in parsed_report: - # assert mandatory fields - assert result.input_file_name == "Dummy" - assert result.gene_symbol == "gyrA" - assert result.gene_name == "gyrA" - assert result.reference_database_name == "pointfinder" - assert result.reference_database_version == "2021-02-01" - assert result.reference_accession == "gyrA p.G81D" - assert result.analysis_software_name == "pointfinder" - assert result.analysis_software_version == "4.1.0" - assert result.genetic_variation_type == "protein_variant_detected" - - assert result.drug_class == "Ciprofloxacin,Nalidixic acid,Ciprofloxacin" - assert result.nucleotide_mutation == "GGT -> GAT" - assert result.amino_acid_mutation == "p.G81D" - def test_resfinder(): metadata = { }