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149 fix missing resistances #179

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merged 3 commits into from
Aug 22, 2024
Merged

149 fix missing resistances #179

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d619fef
Add more blast hits in resistance test data
samuell Jul 11, 2024
4df6d80
Return hits in scraping method and fail test by requiring blaOXA-48
samuell Jul 11, 2024
c169d29
Fix #149 by making regex specific and not matching multiple genes
samuell Jul 11, 2024
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5 changes: 3 additions & 2 deletions microSALT/utils/scraper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -257,9 +257,9 @@ def scrape_blast(self, type="", file_list=[]):
].capitalize()
#Ignores reference name and finds relevant resFinder entry

padder = [x for x in locilengths.keys() if x.startswith('>{}'.format(partials[1]))]
padder = [x for x in locilengths.keys() if x.startswith('>{}_'.format(partials[1]))]
if len(padder) == 0:
padder = [x for x in locilengths.keys() if x.startswith('>{}'.format(partials[1][:-1]))]
padder = [x for x in locilengths.keys() if x.startswith('>{}_'.format(partials[1][:-1]))]
try:
padder = padder[0]
except IndexError as e:
Expand Down Expand Up @@ -438,6 +438,7 @@ def scrape_blast(self, type="", file_list=[]):
self.name, str(e)
)
)
return hypo

def load_resistances(self):
"""Legacy function, loads common resistance names for genes from notes file"""
Expand Down
5 changes: 3 additions & 2 deletions tests/test_scraper.py
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Expand Up @@ -53,8 +53,9 @@ 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
hits = scraper.scrape_blast(type='resistance',file_list=["{}/blast_single_resistance.txt".format(testdata_prefix)])
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genes = [h["gene"] for h in hits]
assert "blaOXA-48" in genes

def test_alignment_scraping(scraper, init_references, testdata_prefix):
scraper.scrape_alignment(file_list=glob.glob("{}/*.stats.*".format(testdata_prefix)))
33 changes: 33 additions & 0 deletions tests/testdata/blast_single_resistance.txt
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Expand Up @@ -31,3 +31,36 @@ ant(6)-Ia_2_KF421157 plus NODE_32_length_3197_cov_303.662317 ant(6)-Ia_2_KF4211
# 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
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