def test_krona(self):
archive = '{"fields": ["gene", "sample", "sequence", "num_hits", "coverage", "taxonomy", "read_names", "nucleotides_aligned", "taxonomy_by_known?"], "singlem_package_sha256s": ["2b2afe0114de20451fccfe74360756376dc83d001d890e84e322ab0833eca6ba", "7f406a73d8bb176994055cb966ff350e208986d12c8215722686c17c26e548c7", "735b44ae547c133163cb7d40f417292c35423864d00c95e7f1b32091b27d46c5", "8fc6dcce2766cc01defb3b5c689a1ed8ce9d59b725c67e58c2044dafaae908b3", "172df49937742b8411d41d217500d862567374401eaf393b25107b22ac630202", "4cb1bf226bf28d8198ed5c29e8a76df411d96a6c3ce1256af16887b9a184b0a6", "d473d3ae677e6e46202461ccdedb2aef23c0a10a3412422586b37e397ca37294", "431a2860bb890cd1c7193c565cbf0cc227850cba36fb17fe94df686e74ee9b11", "faa663527bb9aea63cef03859311f2e7f55fe98590a5ec85c5ba85815a6fd13e", "a0daf111380e6e499ad9c10c3ac413aa9016c7503dd459825100168524bff0d1", "aba631d4735aeb9d2dfbbbfee1c0739bf9e99ad6532a3be04ff627f3e6efdae2", "bba10c1feb0c26bdf46aa3d1dcb992744a699cde5cf02bb2728f8397378b342f", "4d91dd794b25fd256508f0814f6a2d31e20dc85e0aa9ea405031398565276768", "9b23c524a6210af0706eea7252c2d378888029f141b9305c3e88cbac3fd83f88", "50a209417b455a48bc67702d6a3809a172c57f00785d8c705a3322e6e2a71f72"], "version": 1, "alignment_hmm_sha256s": ["dd9b7e283598360b89ec91ff3f5c509361a6108a2eadc44bfb29646b1510f6b7", "b1bb943c3449a78f937db960bfdf6b2bed641388d33fce3cb2d5f69e79946ea6", "de92c90f2c83e380ae3953972fb63fcb8ce868dab87a305f9f1811b84ffb3d39", "453ed4a62608a4aec36117a2dd1a276709ff6b130ecb8d7b1612926bfab25527", "20cc450cf4157ecf1772e0325d4d8ed400b597d888a5cb5044ca69098f935656", "4b0bf5b3d7fd2ca16e54eed59d3a07eab388f70f7078ac096bf415f1c04731d9", "7cbba7ba0ed58d21c7519ba3fcef0abe43378e5c38c985b0d5e0e5219f141d92", "4a3bbe5ac594ef3c7c820e74544828e19eca68bf860d64f928729eb4530fce4e", "06a4bed0a765971b891ca4a4bf5680aeef4a4a249ce0c028798c0e912f0ccfb4", "2678fe218ca860a2d88bdbf76935d8c78a00ab6603a041a432505d754ef08250", "b54ff98aa03ab31af39c737a569b23ee4ed9296c8ea088562bfb3db87c38fe4a", "4ae31f14067bf183f38dca20f2aefb580e5ff25848881dd988908b70b67761bb", "d7bb3d544133f38110a329712b3ace7e7d7c989dafa3815d2d5a292b4c575f50", "7639bb919ef54f7baff3ed3a8c924efca97ed375cf4120a6e05d98fd6ef52cbb", "6923b889888ea34fabf463b2c8ad5fe23c94828f1a2631a07601f246f5e87150"], "otus": [["4.11.ribosomal_protein_L10", "minimal", "TTACGTTCACAATTACGTGAAGCTGGTGTTGAGTATAAAGTATACAAAAACACTATGGTA", 2, 4.878048780487805, "Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus", ["HWI-ST1243:156:D1K83ACXX:7:1106:18671:79482", "HWI-ST1243:156:D1K83ACXX:7:1105:19152:28331"], [60, 60], false], ["4.12.ribosomal_protein_L11_rplK", "minimal", "CCTGCAGGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTG", 4, 9.75609756097561, "Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales", ["HWI-ST1243:156:D1K83ACXX:7:1109:18214:9910", "HWI-ST1243:156:D1K83ACXX:7:1103:21187:63124", "HWI-ST1243:156:D1K83ACXX:7:1108:10813:6928", "HWI-ST1243:156:D1K83ACXX:7:1105:12385:81842"], [60, 60, 60, 60], false]]}'
table_collection = OtuTableCollection()
table_collection.add_archive_otu_table(StringIO(archive))
with tempdir.TempDir() as tmp:
Summariser.summarise(krona_output=os.path.join(tmp, 'KronaOK.html'),
table_collection=table_collection)
self.assertTrue(os.path.exists(os.path.join(tmp,'KronaOK.html')))
def test_krona(self):
archive = '{"fields": ["gene", "sample", "sequence", "num_hits", "coverage", "taxonomy", "read_names", "nucleotides_aligned", "taxonomy_by_known?"], "singlem_package_sha256s": ["2b2afe0114de20451fccfe74360756376dc83d001d890e84e322ab0833eca6ba", "7f406a73d8bb176994055cb966ff350e208986d12c8215722686c17c26e548c7", "735b44ae547c133163cb7d40f417292c35423864d00c95e7f1b32091b27d46c5", "8fc6dcce2766cc01defb3b5c689a1ed8ce9d59b725c67e58c2044dafaae908b3", "172df49937742b8411d41d217500d862567374401eaf393b25107b22ac630202", "4cb1bf226bf28d8198ed5c29e8a76df411d96a6c3ce1256af16887b9a184b0a6", "d473d3ae677e6e46202461ccdedb2aef23c0a10a3412422586b37e397ca37294", "431a2860bb890cd1c7193c565cbf0cc227850cba36fb17fe94df686e74ee9b11", "faa663527bb9aea63cef03859311f2e7f55fe98590a5ec85c5ba85815a6fd13e", "a0daf111380e6e499ad9c10c3ac413aa9016c7503dd459825100168524bff0d1", "aba631d4735aeb9d2dfbbbfee1c0739bf9e99ad6532a3be04ff627f3e6efdae2", "bba10c1feb0c26bdf46aa3d1dcb992744a699cde5cf02bb2728f8397378b342f", "4d91dd794b25fd256508f0814f6a2d31e20dc85e0aa9ea405031398565276768", "9b23c524a6210af0706eea7252c2d378888029f141b9305c3e88cbac3fd83f88", "50a209417b455a48bc67702d6a3809a172c57f00785d8c705a3322e6e2a71f72"], "version": 1, "alignment_hmm_sha256s": ["dd9b7e283598360b89ec91ff3f5c509361a6108a2eadc44bfb29646b1510f6b7", "b1bb943c3449a78f937db960bfdf6b2bed641388d33fce3cb2d5f69e79946ea6", "de92c90f2c83e380ae3953972fb63fcb8ce868dab87a305f9f1811b84ffb3d39", "453ed4a62608a4aec36117a2dd1a276709ff6b130ecb8d7b1612926bfab25527", "20cc450cf4157ecf1772e0325d4d8ed400b597d888a5cb5044ca69098f935656", "4b0bf5b3d7fd2ca16e54eed59d3a07eab388f70f7078ac096bf415f1c04731d9", "7cbba7ba0ed58d21c7519ba3fcef0abe43378e5c38c985b0d5e0e5219f141d92", "4a3bbe5ac594ef3c7c820e74544828e19eca68bf860d64f928729eb4530fce4e", "06a4bed0a765971b891ca4a4bf5680aeef4a4a249ce0c028798c0e912f0ccfb4", "2678fe218ca860a2d88bdbf76935d8c78a00ab6603a041a432505d754ef08250", "b54ff98aa03ab31af39c737a569b23ee4ed9296c8ea088562bfb3db87c38fe4a", "4ae31f14067bf183f38dca20f2aefb580e5ff25848881dd988908b70b67761bb", "d7bb3d544133f38110a329712b3ace7e7d7c989dafa3815d2d5a292b4c575f50", "7639bb919ef54f7baff3ed3a8c924efca97ed375cf4120a6e05d98fd6ef52cbb", "6923b889888ea34fabf463b2c8ad5fe23c94828f1a2631a07601f246f5e87150"], "otus": [["4.11.ribosomal_protein_L10", "minimal", "TTACGTTCACAATTACGTGAAGCTGGTGTTGAGTATAAAGTATACAAAAACACTATGGTA", 2, 4.878048780487805, "Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus", ["HWI-ST1243:156:D1K83ACXX:7:1106:18671:79482", "HWI-ST1243:156:D1K83ACXX:7:1105:19152:28331"], [60, 60], false], ["4.12.ribosomal_protein_L11_rplK", "minimal", "CCTGCAGGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTG", 4, 9.75609756097561, "Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales", ["HWI-ST1243:156:D1K83ACXX:7:1109:18214:9910", "HWI-ST1243:156:D1K83ACXX:7:1103:21187:63124", "HWI-ST1243:156:D1K83ACXX:7:1108:10813:6928", "HWI-ST1243:156:D1K83ACXX:7:1105:12385:81842"], [60, 60, 60, 60], false]]}'
table_collection = OtuTableCollection()
table_collection.add_archive_otu_table(StringIO(archive))
with tempdir.TempDir() as tmp:
Summariser.summarise(krona_output=os.path.join(tmp, 'KronaOK.html'),
table_collection=table_collection)
self.assertTrue(os.path.exists(os.path.join(tmp,'KronaOK.html')))
def test_wide_format(self):
e = [
['gene', 'sample', 'sequence', 'num_hits', 'coverage', 'taxonomy'],
[
'4.11.ribosomal_protein_L10', 'minimal',
'TTACGTTCACAATTACGTGAAGCTGGTGTTGAGTATAAAGTATACAAAAACACTATGGTA',
'2', '4.88',
'Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus'
],
[
'4.12.ribosomal_protein_L11_rplK', 'minimal',
'CCTGCAGGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTG',
'4', '9.76',
'Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales'
],
[
'4.11.ribosomal_protein_L10', 'maximal',
'TTACGTTCACAATTACGTGAAGCTGGTGTTGAGTATAAAGTATACAAAAACACTATGGTA',
'2', '4.88',
'Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus'
]
]
exp = "\n".join(["\t".join(x) for x in e] + [''])
output = StringIO()
table_collection = OtuTableCollection()
table_collection.add_otu_table(StringIO(exp))
Summariser().write_wide_format_otu_table(
table_collection=table_collection, output_table_io=output)
self.assertEqual(
'marker\tsequence\tminimal\tmaximal\ttaxonomy\n4.11.ribosomal_protein_L10\tTTACGTTCACAATTACGTGAAGCTGGTGTTGAGTATAAAGTATACAAAAACACTATGGTA\t2\t2\tRoot; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus\n4.12.ribosomal_protein_L11_rplK\tCCTGCAGGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTG\t4\t0\tRoot; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales\n',
output.getvalue())