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Adjusted pytest to include the required folders in the pythonpath
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,58 +1,61 @@ | ||
| import importlib | ||
| import unittest | ||
| import os | ||
|
|
||
| from pathlib import Path | ||
|
|
||
| script_dir = Path(__file__).resolve().parent | ||
| uniprot_dir = script_dir / '../../helpers/database-import-scripts/uniprot' | ||
| uniprot_dir = uniprot_dir.resolve() | ||
|
|
||
| preprocess_taxonomy = importlib.import_module("helpers.database-import-scripts.uniprot.preprocess_taxonomy_for_uniprot") | ||
| parse_metadata =preprocess_taxonomy.parse_metadata | ||
| match_taxid_to_gca = preprocess_taxonomy.match_taxid_to_gca | ||
| get_species_level_taxonomy = preprocess_taxonomy.get_species_level_taxonomy | ||
| from helpers.database_import_scripts.uniprot.preprocess_taxonomy_for_uniprot import ( | ||
| get_species_level_taxonomy, | ||
| match_taxid_to_gca, | ||
| parse_metadata, | ||
| ) | ||
|
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||
|
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| class TestPreprocessTaxonomyForUniprot(unittest.TestCase): | ||
| def setUp(self): | ||
| self.metadata_file = os.path.join(script_dir, "fixtures", "preprocess_taxonomy_for_uniprot", | ||
| "sample_metadata.tsv") | ||
| self.metadata_file = ( | ||
| Path(__file__).resolve().parent | ||
| / "fixtures/preprocess_taxonomy_for_uniprot/sample_metadata.tsv" | ||
| ) | ||
| self.gca_accessions, self.sample_accessions = parse_metadata(self.metadata_file) | ||
| self.mgyg_to_gca, self.gca_to_taxid = match_taxid_to_gca(self.gca_accessions, self.sample_accessions, 2) | ||
| self.mgyg_to_gca, self.gca_to_taxid = match_taxid_to_gca( | ||
| self.gca_accessions, self.sample_accessions, 2 | ||
| ) | ||
|
|
||
| def test_match_taxid_to_gca(self): | ||
| expected_gca_to_taxid = {'GCA_946182765': '370804', | ||
| 'GCA_946182785': '244328', | ||
| 'GCA_946182825': '297314', | ||
| 'GCA_946182815': '370804', | ||
| 'GCA_946182805': '190764', | ||
| 'GCA_946182835': '370804', | ||
| 'GCA_946183145': '1678694', | ||
| 'GCA_946183335': '157472'} | ||
| expected_mgyg_to_gca = {'MGYG000304400': 'GCA_946182765', | ||
| 'MGYG000304401': 'GCA_946182785', | ||
| 'MGYG000304403': 'GCA_946182825', | ||
| 'MGYG000304404': 'GCA_946182815', | ||
| 'MGYG000304405': 'GCA_946182805', | ||
| 'MGYG000304406': 'GCA_946182835', | ||
| 'MGYG000304407': 'GCA_946183145', | ||
| 'MGYG000304408': 'GCA_946183335'} | ||
| expected_gca_to_taxid = { | ||
| "GCA_946182765": "370804", | ||
| "GCA_946182785": "244328", | ||
| "GCA_946182825": "297314", | ||
| "GCA_946182815": "370804", | ||
| "GCA_946182805": "190764", | ||
| "GCA_946182835": "370804", | ||
| "GCA_946183145": "1678694", | ||
| "GCA_946183335": "157472", | ||
| } | ||
| expected_mgyg_to_gca = { | ||
| "MGYG000304400": "GCA_946182765", | ||
| "MGYG000304401": "GCA_946182785", | ||
| "MGYG000304403": "GCA_946182825", | ||
| "MGYG000304404": "GCA_946182815", | ||
| "MGYG000304405": "GCA_946182805", | ||
| "MGYG000304406": "GCA_946182835", | ||
| "MGYG000304407": "GCA_946183145", | ||
| "MGYG000304408": "GCA_946183335", | ||
| } | ||
| self.assertEqual(self.mgyg_to_gca, expected_mgyg_to_gca) | ||
| self.assertEqual(self.gca_to_taxid, expected_gca_to_taxid) | ||
|
|
||
| def test_get_species_level_taxonomy(self): | ||
| taxid1, name1, submittable1, lineage1 = get_species_level_taxonomy( | ||
| "k__Bacteria;p__Bacillota_I;c__Bacilli_A;o__RFN20;f__CAG-826;g__UBA3207;s__UBA3207 sp946183335") | ||
| self.assertEqual(lineage1, "d__Bacteria;p__Bacillota_I;c__Bacilli_A;o__RFN20;f__CAG-826;g__UBA3207;s__UBA3207 sp946183335") | ||
| _, name1, submittable1, lineage1 = get_species_level_taxonomy( | ||
| "k__Bacteria;p__Bacillota_I;c__Bacilli_A;o__RFN20;f__CAG-826;g__UBA3207;s__UBA3207 sp946183335" | ||
| ) | ||
| self.assertEqual( | ||
| lineage1, | ||
| "d__Bacteria;p__Bacillota_I;c__Bacilli_A;o__RFN20;f__CAG-826;g__UBA3207;s__UBA3207 sp946183335", | ||
| ) | ||
| self.assertEqual(submittable1, False) | ||
| self.assertEqual(name1, "UBA3207 sp946183335") | ||
|
|
||
| taxid2, name2, submittable2, lineage2 = get_species_level_taxonomy( | ||
| "d__Bacteria; p__Pseudomonadota; c__Gammaproteobacteria; o__Enterobacterales; f__Enterobacteriaceae; g__Escherichia; s__Escherichia coli") | ||
|
|
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| taxid2, _, submittable2, _ = get_species_level_taxonomy( | ||
| "d__Bacteria; p__Pseudomonadota; c__Gammaproteobacteria; o__Enterobacterales; f__Enterobacteriaceae; g__Escherichia; s__Escherichia coli" | ||
| ) | ||
| self.assertEqual(submittable2, True) | ||
| self.assertEqual(taxid2, '562') | ||
|
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| self.assertEqual(taxid2, "562") |