Remove pointfinder tests

pha4ge · Dec 30, 2024 · 2127e9a · 2127e9a
1 parent b179b3c
commit 2127e9a
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diff --git 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
@@ -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 = {
     }