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Add testdata to fail OXA-48 test
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@samuell
samuell committed Jul 11, 2024
1 parent e00b092 commit 09ad8a4
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Showing 4 changed files with 69 additions and 36 deletions.
2 changes: 1 addition & 1 deletion setup.py
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Expand Up @@ -23,7 +23,7 @@
zip_safe=False,
data_files=[('expec', ['unique_references/ExPEC.fsa']),
('logos', ['artwork/microsalt.jpg', 'artwork/swedac.jpg']),
('testdata', ['tests/testdata/sampleinfo_samples.json','tests/testdata/sampleinfo_mlst.json','tests/testdata/sampleinfo_projects.json','tests/testdata/sampleinfo_reports.json','tests/testdata/sampleinfo_expec.json','tests/testdata/sampleinfo_resistance.json','tests/testdata/quast_results.tsv', 'tests/testdata/blast_single_resistance.txt','tests/testdata/blast_single_loci.txt','tests/testdata/alignment.stats.ref','tests/testdata/alignment.stats.raw','tests/testdata/alignment.stats.map','tests/testdata/alignment.stats.ins','tests/testdata/alignment.stats.dup','tests/testdata/alignment.stats.cov','configExample.json']),
('testdata', ['tests/testdata/sampleinfo_samples.json','tests/testdata/sampleinfo_mlst.json','tests/testdata/sampleinfo_projects.json','tests/testdata/sampleinfo_reports.json','tests/testdata/sampleinfo_expec.json','tests/testdata/sampleinfo_resistance.json','tests/testdata/quast_results.tsv', 'tests/testdata/blast_resistances.txt','tests/testdata/blast_single_loci.txt','tests/testdata/alignment.stats.ref','tests/testdata/alignment.stats.raw','tests/testdata/alignment.stats.map','tests/testdata/alignment.stats.ins','tests/testdata/alignment.stats.dup','tests/testdata/alignment.stats.cov','configExample.json']),
('tests/testdata/AAA1234_2000.1.2_3.4.5/AAA1234A1/', ['tests/testdata/AAA1234_2000.1.2_3.4.5/AAA1234A1/dummysequences_1.fastq.gz', 'tests/testdata/AAA1234_2000.1.2_3.4.5/AAA1234A1/dummysequences_2.fastq.gz']),
('tests/testdata/AAA1234_2000.1.2_3.4.5/AAA1234A2/', ['tests/testdata/AAA1234_2000.1.2_3.4.5/AAA1234A2/dummysequences_1.fastq.gz', 'tests/testdata/AAA1234_2000.1.2_3.4.5/AAA1234A2/dummysequences_2.fastq.gz']),
('tests/testdata/AAA1234_2000.1.2_3.4.5/AAA1234A3/', ['tests/testdata/AAA1234_2000.1.2_3.4.5/AAA1234A3/dummysequences_1.fastq.gz', 'tests/testdata/AAA1234_2000.1.2_3.4.5/AAA1234A3/dummysequences_2.fastq.gz']),
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4 changes: 2 additions & 2 deletions tests/test_scraper.py
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Expand Up @@ -53,8 +53,8 @@ def test_blast_scraping(scraper, testdata_prefix, caplog):
scraper.scrape_blast(type='seq_type',file_list=["{}/blast_single_loci.txt".format(testdata_prefix)])
assert "candidate" in caplog.text
caplog.clear()
scraper.scrape_blast(type='resistance',file_list=["{}/blast_single_resistance.txt".format(testdata_prefix)])
assert "candidate" in caplog.text
scraper.scrape_blast(type='resistance',file_list=["{}/blast_resistances.txt".format(testdata_prefix)])
assert "OXA-48" in caplog.text

def test_alignment_scraping(scraper, init_references, testdata_prefix):
scraper.scrape_alignment(file_list=glob.glob("{}/*.stats.*".format(testdata_prefix)))
66 changes: 66 additions & 0 deletions tests/testdata/blast_resistances.txt
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@@ -0,0 +1,66 @@
# BLASTN 2.9.0+
# Query: NODE_31_length_3240_cov_286.006593
# Database: /tmp/aminoglycoside
# 0 hits found
# BLASTN 2.9.0+
# Query: NODE_32_length_3197_cov_303.662317
# Database: /tmp/aminoglycoside
# Fields: subject title, subject strand, query acc.ver, subject acc.ver, % identity, evalue, bit score, q. start, q. end, s. start, s. end, alignment length
# 7 hits found
aph(3')-III_1_M26832 plus NODE_32_length_3197_cov_303.662317 aph(3')-III_1_M26832 100.000 0.0 1469 1392 2186 1 795 795
aph(3')-IIIa_2_AJ490186 plus NODE_32_length_3197_cov_303.662317 aph(3')-IIIa_2_AJ490186 99.874 0.0 1463 1392 2186 1 795 795
aph(3')-IIIa_1_AF330699 plus NODE_32_length_3197_cov_303.662317 aph(3')-IIIa_1_AF330699 99.874 0.0 1463 1392 2186 1 795 795
aph(3')-IIIa_3_AB247327 plus NODE_32_length_3197_cov_303.662317 aph(3')-IIIa_3_AB247327 99.372 0.0 1441 1392 2186 1 795 796
ant(6)-Ia_1_AF330699 plus NODE_32_length_3197_cov_303.662317 ant(6)-Ia_1_AF330699 99.688 0.0 1173 131 772 269 909 642
ant(6)-Ia_5_AB247327 plus NODE_32_length_3197_cov_303.662317 ant(6)-Ia_5_AB247327 99.377 0.0 1162 131 772 269 909 642
ant(6)-Ia_2_KF421157 plus NODE_32_length_3197_cov_303.662317 ant(6)-Ia_2_KF421157 84.201 1.28e-159 556 131 705 269 842 576
# BLASTN 2.9.0+
# Query: NODE_33_length_3121_cov_306.530985
# Database: /tmp/aminoglycoside
# 0 hits found
# BLASTN 2.9.0+
# Query: NODE_34_length_1659_cov_289.301746
# Database: /tmp/aminoglycoside
# 0 hits found
# BLASTN 2.9.0+
# Query: NODE_35_length_1618_cov_2.178503
# Database: /tmp/aminoglycoside
# 0 hits found
# BLASTN 2.9.0+
# Query: NODE_36_length_1210_cov_161.702165
# Database: /tmp/aminoglycoside
# 0 hits found
# BLAST processed 215 queries
# BLASTN 2.12.0+
# Query: NODE_65_length_2231_cov_99.410745
# Database: /tmp/beta-lactam
# Fields: subject title, subject strand, query acc.ver, subject acc.ver, % identity, evalue, bit score, q. start, q. end, s. start, s. end, alignment length
# 28 hits found
blaOXA-48_1_AY236073 minus NODE_65_length_2231_cov_99.410745 blaOXA-48_1_AY236073 100.000 0.0 1474 1409 2206 798 1 798
blaOXA-566_1_MF099636 minus NODE_65_length_2231_cov_99.410745 blaOXA-566_1_MF099636 99.875 0.0 1469 1409 2206 798 1 798
blaOXA-244_1_KP659189 minus NODE_65_length_2231_cov_99.410745 blaOXA-244_1_KP659189 99.875 0.0 1469 1409 2206 798 1 798
blaOXA-162_1_GU197550 minus NODE_65_length_2231_cov_99.410745 blaOXA-162_1_GU197550 99.875 0.0 1469 1409 2206 798 1 798
blaOXA-519_1_KX349732 minus NODE_65_length_2231_cov_99.410745 blaOXA-519_1_KX349732 99.875 0.0 1469 1409 2206 798 1 798
blaOXA-505_1_KU531433 minus NODE_65_length_2231_cov_99.410745 blaOXA-505_1_KU531433 99.875 0.0 1469 1409 2206 798 1 798
blaOXA-245_1_JX438001 minus NODE_65_length_2231_cov_99.410745 blaOXA-245_1_JX438001 99.749 0.0 1463 1409 2206 798 1 798
blaOXA-370_1_KJ488943 minus NODE_65_length_2231_cov_99.410745 blaOXA-370_1_KJ488943 99.624 0.0 1458 1409 2206 798 1 798
blaOXA-199_1_JN704570 minus NODE_65_length_2231_cov_99.410745 blaOXA-199_1_JN704570 99.373 0.0 1447 1409 2206 798 1 798
blaOXA-252_1_NG_050608 minus NODE_65_length_2231_cov_99.410745 blaOXA-252_1_NG_050608 99.248 0.0 1441 1409 2206 798 1 798
blaOXA-515_1_KU866383 minus NODE_65_length_2231_cov_99.410745 blaOXA-515_1_KU866383 99.248 0.0 1441 1409 2206 798 1 798
blaOXA-517_1_KU878974 minus NODE_65_length_2231_cov_99.410745 blaOXA-517_1_KU878974 99.248 0.0 1435 1409 2206 792 1 798
blaOXA-204_1_KP027885 minus NODE_65_length_2231_cov_99.410745 blaOXA-204_1_KP027885 98.997 0.0 1430 1409 2206 798 1 798
blaOXA-546_1_KY682756 minus NODE_65_length_2231_cov_99.410745 blaOXA-546_1_KY682756 98.872 0.0 1424 1409 2206 798 1 798
blaOXA-547_1_KY684124 minus NODE_65_length_2231_cov_99.410745 blaOXA-547_1_KY684124 98.622 0.0 1413 1409 2206 798 1 798
blaOXA-438_1_KP410734 minus NODE_65_length_2231_cov_99.410745 blaOXA-438_1_KP410734 98.747 0.0 1413 1409 2206 792 1 798
blaOXA-405_1_KM589641 minus NODE_65_length_2231_cov_99.410745 blaOXA-405_1_KM589641 98.496 0.0 1397 1409 2206 786 1 798
blaOXA-247_1_JX893517 minus NODE_65_length_2231_cov_99.410745 blaOXA-247_1_JX893517 98.371 0.0 1391 1409 2206 786 1 798
blaOXA-163_1_HQ700343 minus NODE_65_length_2231_cov_99.410745 blaOXA-163_1_HQ700343 98.371 0.0 1391 1409 2206 786 1 798
blaOXA-439_1_KP727573 minus NODE_65_length_2231_cov_99.410745 blaOXA-439_1_KP727573 98.246 0.0 1386 1409 2206 786 1 798
blaOXA-514_1_KU866382 minus NODE_65_length_2231_cov_99.410745 blaOXA-514_1_KU866382 97.870 0.0 1380 1409 2206 798 1 798
blaOXA-538_1_KX827284 minus NODE_65_length_2231_cov_99.410745 blaOXA-538_1_KX827284 97.750 0.0 1375 1409 2206 798 1 800
blaOXA-416_1_KP264119 minus NODE_65_length_2231_cov_99.410745 blaOXA-416_1_KP264119 96.992 0.0 1341 1409 2206 798 1 798
blaOXA-181_1_CM004561 minus NODE_65_length_2231_cov_99.410745 blaOXA-181_1_CM004561 94.493 0.0 1230 1409 2206 798 1 799
blaOXA-232_1_JX423831 minus NODE_65_length_2231_cov_99.410745 blaOXA-232_1_JX423831 94.368 0.0 1225 1409 2206 798 1 799
blaOXA-484_1_KR401105 minus NODE_65_length_2231_cov_99.410745 blaOXA-484_1_KR401105 94.368 0.0 1225 1409 2206 798 1 799
blaOXA-535_1_KX828709 minus NODE_65_length_2231_cov_99.410745 blaOXA-535_1_KX828709 84.856 0.0 804 1409 2206 798 1 799
blaOXA-436_1_KT959105 minus NODE_65_length_2231_cov_99.410745 blaOXA-436_1_KT959105 84.481 0.0 787 1409 2206 798 1 799
33 changes: 0 additions & 33 deletions tests/testdata/blast_single_resistance.txt
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