diff --git a/setup.py b/setup.py index 7de35ffb..ffeedf18 100644 --- a/setup.py +++ b/setup.py @@ -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']), diff --git a/tests/test_scraper.py b/tests/test_scraper.py index c4b5718b..ac9ad6ab 100644 --- a/tests/test_scraper.py +++ b/tests/test_scraper.py @@ -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))) diff --git a/tests/testdata/blast_resistances.txt b/tests/testdata/blast_resistances.txt new file mode 100644 index 00000000..dcb405ac --- /dev/null +++ b/tests/testdata/blast_resistances.txt @@ -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 diff --git a/tests/testdata/blast_single_resistance.txt b/tests/testdata/blast_single_resistance.txt deleted file mode 100644 index b8cf46c8..00000000 --- a/tests/testdata/blast_single_resistance.txt +++ /dev/null @@ -1,33 +0,0 @@ -# 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