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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,4 @@ | ||
| >VFDB_test 90~~~90~~~90~~~yaxA~~~cytotoxin YaxA~~~VFDB:VFG045347,VFDB:VF0511 | ||
| MTQTQLAIDNVLASAENTIQLNELPKVVLDFITGEQTSVARSGGIFTKEDLINLKLYVRKGLSLPTRQDEVEAYLGYKKIDVAGLEPKDIKLLFDEIHNHALNWNDVEQAVLQQSLDLDIAAKNIISTGNEIINLINQMPITLRVKTLLRDITDKQLENITYESADHEVASALKDILDDMKGDINRHQTTTENVRKKVSDYRITLTGGELSSGDKVNGLEPQVKTKYDLMEKSNMRKSIKELDEKIKEKKQRIEQLKKDYDKFVGLSFTGAIGGIIAMAITSGIFGAKAENARKEKNALISEVAELESKVSSQRALQTALEALSLSFSDIGIRMVDAESALNHLDFMWLSVLNQITESQIQFAMINNALRLTSFVNKFQQVITPWQSVGDSARQLVDIFDEAIKEYKKVYG | ||
| >hypo-mock-test 99~~~99~~~99~~~mock1~~~mock hypothetical user protein 1~~~USERDB:MOCK1 | ||
| MAQNPFKALNINIDKIESALTQNGVTNYSSNVKNERETHISGTYKGIDFLIKLMPSGGNTTIGRASGQNNTYFDEIALIIKENCLYSDTKNFEYTIPKFSDDDRANLFEFLSEEGITITEDNNNDPNCKHQYIMTTSNGDRVRAKIYKRGSIQFQGKYLQIASLINDFMCSILNMKEIVEQKNKEFNVDIKKETIESELHSKLPKSIDKIHEDIKKQLSCSLIMKKIDVEMEDYSTYCFSALRAIEGFIYQILNDVCNPSSSKNLGEYFTENKPKYIIREIHQETINGEIAEVLCECYTYWHENRHGLFHMKPGIADTKTINKLESIAIIDTVCQLIDGGVARLKL |
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| import json | ||
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| from pathlib import Path | ||
| from subprocess import run | ||
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| import bakta.config as cfg | ||
| import bakta.expert.protein_sequences as exp_aa_seq | ||
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| import pytest | ||
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| SEQUENCE = 'MRADEEPGDLSAVAQDYLKVIWTAQEWSQDKVSTKMLAERIGVSASTASESIRKLAEQGLVDHEKYGAVTLTDSGRRAALAMVRRHRLLETFLVNELGYRWDEVHDEA' | ||
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| aa_min = { | ||
| 'id': 'min', | ||
| 'description': '~~~product~~~', | ||
| 'sequence': SEQUENCE | ||
| } | ||
| aa_min_gene = { | ||
| 'id': 'min', | ||
| 'description': 'gene~~~product~~~', | ||
| 'sequence': SEQUENCE | ||
| } | ||
| aa_min_dbxref = { | ||
| 'id': 'min', | ||
| 'description': 'gene~~~product~~~db-1:id-1', | ||
| 'sequence': SEQUENCE | ||
| } | ||
| aa_min_dbxrefs = { | ||
| 'id': 'min', | ||
| 'description': 'gene~~~product~~~db-1:id-1,db-2:id-2', | ||
| 'sequence': SEQUENCE | ||
| } | ||
| aa_full = { | ||
| 'id': 'full', | ||
| 'description': '90.0~~~80.0~~~80.0~~~gene~~~product~~~db-1:id-1,db-2:id-2', | ||
| 'sequence': SEQUENCE | ||
| } | ||
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| aa_wrong_1 = { | ||
| 'id': 'low-cols', | ||
| 'description': '~~~product', | ||
| 'sequence': SEQUENCE | ||
| } | ||
| aa_wrong_2 = { | ||
| 'id': 'high-cols', | ||
| 'description': '90~~~80~~~80~~~gene~~~product~~~dbxref:dbxref~~~', | ||
| 'sequence': SEQUENCE | ||
| } | ||
| aa_wrong_3 = { | ||
| 'id': 'no-product', | ||
| 'description': 'gene~~~~~~dbxref:dbxref', | ||
| 'sequence': SEQUENCE | ||
| } | ||
| aa_wrong_4 = { | ||
| 'id': 'no-product-full', | ||
| 'description': '90~~~80~~~80~~~gene~~~~~~dbxref:dbxref', | ||
| 'sequence': SEQUENCE | ||
| } | ||
| aa_wrong_5 = { | ||
| 'id': 'wrong-dbxref', | ||
| 'description': 'gene~~~product~~~dbxrefdbxref', | ||
| 'sequence': SEQUENCE | ||
| } | ||
| aa_wrong_6 = { | ||
| 'id': 'wrong-dbxref-full', | ||
| 'description': '90~~~80~~~80~~~gene~~~product~~~dbxrefdbxref', | ||
| 'sequence': SEQUENCE | ||
| } | ||
| aa_wrong_7 = { | ||
| 'id': 'wrong-id', | ||
| 'description': 'ninety~~~80~~~80~~~gene~~~product~~~dbxref:dbxref', | ||
| 'sequence': SEQUENCE | ||
| } | ||
| aa_wrong_8 = { | ||
| 'id': 'wrong-min-query-cov', | ||
| 'description': '90~~~eighty~~~80~~~gene~~~product~~~dbxref:dbxref', | ||
| 'sequence': SEQUENCE | ||
| } | ||
| aa_wrong_9 = { | ||
| 'id': 'wrong-min-model-cov', | ||
| 'description': '90~~~80~~~eighty~~~gene~~~product~~~dbxref:dbxref', | ||
| 'sequence': SEQUENCE | ||
| } | ||
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| @pytest.mark.parametrize( | ||
| "aa", | ||
| [ | ||
| (aa_wrong_1), | ||
| (aa_wrong_2), | ||
| (aa_wrong_3), | ||
| (aa_wrong_4), | ||
| (aa_wrong_5), | ||
| (aa_wrong_6), | ||
| (aa_wrong_7), | ||
| (aa_wrong_8), | ||
| (aa_wrong_9) | ||
| ] | ||
| ) | ||
| def test_wrong_user_proteins_io(tmpdir, aa): | ||
| tmpdir = Path(tmpdir) | ||
| cfg.user_proteins = tmpdir.joinpath('user.faa') | ||
| write_tmp_faa(aa, cfg.user_proteins) | ||
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| user_proteins_path = tmpdir.joinpath('user-clean.faa') | ||
| with pytest.raises(SystemExit) as pytest_wrapped_e: | ||
| exp_aa_seq.write_user_protein_sequences(user_proteins_path) | ||
| assert pytest_wrapped_e.type == SystemExit | ||
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| @pytest.mark.parametrize( | ||
| "aa", | ||
| [ | ||
| (aa_min), | ||
| (aa_min_gene), | ||
| (aa_min_dbxref), | ||
| (aa_min_dbxrefs), | ||
| (aa_full) | ||
| ] | ||
| ) | ||
| def test_user_proteins_io(tmpdir, aa): | ||
| tmpdir = Path(tmpdir) | ||
| cfg.user_proteins = tmpdir.joinpath('user.faa') | ||
| write_tmp_faa(aa, cfg.user_proteins) | ||
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| user_proteins_path = tmpdir.joinpath('user-clean.faa') | ||
| exp_aa_seq.write_user_protein_sequences(user_proteins_path) | ||
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| def write_tmp_faa(aa, aa_path): | ||
| with aa_path.open('w') as fh: | ||
| fh.write(f">{aa['id']} {aa['description']}\n") | ||
| fh.write(aa['sequence']) | ||
| fh.write('\n') | ||
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| @pytest.mark.slow | ||
| def test_user_proteins(tmpdir): | ||
| # fast test skipping all feature detections | ||
| proc = run( | ||
| [ | ||
| 'bin/bakta', '--db', 'test/db', '--output', tmpdir, '--prefix', 'test', '--proteins', 'test/data/user-proteins.faa', | ||
| '--skip-tmrna', '--skip-trna', '--skip-rrna', '--skip-ncrna', '--skip-ncrna-region', '--skip-crispr', '--skip-sorf', '--skip-ori', '--skip-gap', | ||
| 'test/data/NC_002127.1.fna' | ||
| ] | ||
| ) | ||
| assert proc.returncode == 0 | ||
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| tmpdir_path = Path(tmpdir) | ||
| results_path = Path(tmpdir_path.joinpath('test.json')) | ||
| assert Path.exists(results_path) | ||
| results = None | ||
| with results_path.open() as fh: | ||
| results = json.load(fh) | ||
| assert results is not None | ||
| user_prot_feats = [] | ||
| for feat in results['features']: | ||
| if('expert' in feat and 'user_proteins' in feat['expert']): | ||
| user_prot_feats.append(feat) | ||
| assert len(user_prot_feats) == 1 |