def test_no_cluster(self):
e = [
['gene', 'sample', 'sequence', 'num_hits', 'coverage', 'taxonomy'],
[
'4.11.ribosomal_protein_L10', 'minimal',
'TTACGTTCACAATTACGTGAAGCTGGTGTTGAGTATAAAGTATACAAAAACACT', '2',
'4.88',
'Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus'
],
[
'4.12.ribosomal_protein_L11_rplK', 'minimal',
'TTACGTTCACAATTACGTGAAGCTGGTGTTGAGTATAAAGTATACAAAAACACA', '4',
'9.76',
'Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales'
]
]
exp = "\n".join(["\t".join(x) for x in e] + [''])
table_collection = OtuTableCollection()
table_collection.add_otu_table(StringIO(exp))
clusters = list(Clusterer().each_cluster(table_collection, 1.0))
self.assertEqual(2, len(clusters))
self.assertIsInstance(clusters[0], SampleWiseClusteredOtu)
sorted_clusters = list(sorted(clusters, key=lambda x: x.count))
c = sorted_clusters[0]
self.assertEqual(2, c.count)
self.assertEqual(4.88, c.coverage)
c = sorted_clusters[1]
self.assertEqual(4, c.count)
self.assertEqual(9.76, c.coverage)
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())
def test_archive_to_otu_table_conversion(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]]}'
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'
]
]
exp = "\n".join(["\t".join(x) for x in e] + [''])
output = StringIO()
table_collection = OtuTableCollection()
table_collection.add_archive_otu_table(StringIO(archive))
Summariser().write_otu_table(table_collection=table_collection,
output_table_io=output,
output_extras=False)
self.assertEqual(exp, output.getvalue())
def test_multiple_genes_and_samples(self):
a = [self.headers,['2.12.ribosomal_protein_L11_rplK.gpkg','minimal','GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC','7','17.07','Root; d__Archaea; p__Firmicutes; c__Bacilli; o__Bacillales'],
['2.12.ribosomal_protein_L11_rplK.gpkg','minimal','AGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC','9','18.07','Root; d__Bacteria'],
['2.12.ribosomal_protein_L11_rplK.gpkg','minimal','GAAAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC','8','17.57','Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales'],
['2.13.ribosomal_protein_L11_rplK.gpkg','minimal','GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC','9','18.07','Root; d__Archaea; p__Firmicutes; c__Bacilli; o__Bacillales'],
['2.13.ribosomal_protein_L11_rplK.gpkg','minimal','AGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC','8','17.57','Root; d__Bacteria'],
['2.13.ribosomal_protein_L11_rplK.gpkg','minimal','GAAAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC','7','17.07','Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales'],
['2.12.ribosomal_protein_L11_rplK.gpkg','minimal2','GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC','7','17.07','Root; d__Archaea; p__Firmicutes; c__Bacilli; o__Bacillales'],
['2.12.ribosomal_protein_L11_rplK.gpkg','minimal2','AGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC','9','18.07','Root; d__Bacteria'],
['2.12.ribosomal_protein_L11_rplK.gpkg','minimal2','GAAAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC','8','17.57','Root; d__Aacteria; p__Firmicutes; c__Bacilli; o__Bacillales'],
]
table = "\n".join(["\t".join(x) for x in a]+[''])
e = [self.output_headers,
['reference','2.12.ribosomal_protein_L11_rplK.gpkg','minimal','0','AGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC','9','18.07','Root; d__Bacteria'],
['strain','2.12.ribosomal_protein_L11_rplK.gpkg','minimal','3','GAAAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC','8','17.57','Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales'],
['reference','2.13.ribosomal_protein_L11_rplK.gpkg','minimal','0','AGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC','8','17.57','Root; d__Bacteria'],
['strain','2.13.ribosomal_protein_L11_rplK.gpkg','minimal','3','GAAAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC','7','17.07','Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales'],
['reference','2.12.ribosomal_protein_L11_rplK.gpkg','minimal2','0','AGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC','9','18.07','Root; d__Bacteria'],
]
exp = "\n".join(["\t".join(x) for x in e]+[''])
output = StringIO()
table_collection = OtuTableCollection()
table_collection.set_target_taxonomy_by_string('Root; d__Bacteria')
table_collection.add_otu_table(StringIO(table))
StrainSummariser().summarise_strains(\
table_collection = table_collection,
output_table_io = output)
self.assertEqual(exp, output.getvalue())
def test_not_enough_samples(self):
e = [
['gene', 'sample', 'sequence', 'num_hits', 'coverage', 'taxonomy'],
[
'4.11.ribosomal_protein_L10', 'minimal',
'TTACGTTCACAATTACGTGAAGCTGGTGTTGAGTATAAAGTATACAAAAACACTATGGTA',
'1', '4.88',
'Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus'
],
[
'4.12.ribosomal_protein_L11_rplK', 'minimal',
'TTACGTTCACAATTACGTGAAGCTGGTGTTGAGTATAAAGTATACAAAAACACTATGGTT',
'2', '9.76',
'Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales'
]
]
exp = "\n".join(["\t".join(x) for x in e] + [''])
table_collection = OtuTableCollection()
table_collection.add_otu_table(StringIO(exp))
rares = Rarefier().rarefy(
table_collection, 2, random_generator=PredictableRandomGenerator())
self.assertIsInstance(rares, OtuTable)
rares = list(rares)
self.assertEqual(1, len(rares))
self.assertEqual(
'TTACGTTCACAATTACGTGAAGCTGGTGTTGAGTATAAAGTATACAAAAACACTATGGTT',
rares[0].sequence)
self.assertEqual([2], [e.count for e in rares])
def test_cycle(self):
otu_table = \
[['gene','sample','sequence','num_hits','coverage','taxonomy'],
['ribosomal_protein_L11_rplK_gpkg','minimal','GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC','7','14.4',
'Root; k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales'],
['ribosomal_protein_S2_rpsB_gpkg','minimal','CGTCGTTGGAACCCAAAAATGAAAAAATATATCTTCACTGAGAGAAATGGTATTTATATC','6','12.2',
'Root; k__Bacteria; p__Firmicutes; c__Bacilli'],
['ribosomal_protein_S17_gpkg','minimal','GCTAAATTAGGAGACATTGTTAAAATTCAAGAAACTCGTCCTTTATCAGCAACAAAACGT','9','18.8',
'Root; k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus']]
otu_table = "\n".join(["\t".join(x) for x in otu_table])
with tempdir.TempDir() as tmp:
db_path = os.path.join(tmp, 'my.sdb')
collection = OtuTableCollection()
collection.add_otu_table(StringIO.StringIO(otu_table))
SequenceDatabase.create_from_otu_table(db_path, collection)
db2 = SequenceDatabase.acquire(db_path)
s1 = db2.extract_sequence(1)
self.assertEqual('ribosomal_protein_L11_rplK_gpkg', s1.marker)
self.assertEqual('minimal',s1.sample_name)
self.assertEqual('GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC',s1.sequence)
self.assertEqual(7, s1.count)
self.assertEqual('Root; k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales', s1.taxonomy)
s3 = db2.extract_sequence(3)
self.assertEqual('GCTAAATTAGGAGACATTGTTAAAATTCAAGAAACTCGTCCTTTATCAGCAACAAAACGT',s3.sequence)
self.assertEqual('Root; k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus', s3.taxonomy)
self.assertEqual(os.path.join(db_path,"sequences.fasta"), db2.sequences_fasta_file)
def test_nothing_returned(self):
e = [['gene','sample','sequence','num_hits','coverage','taxonomy']]
exp = "\n".join(["\t".join(x) for x in e]+[''])
table_collection = OtuTableCollection()
table_collection.add_otu_table(StringIO(exp))
self.assertEqual(0, len(list(table_collection)))
rares = Rarefier().rarefy(table_collection, 0)
self.assertEqual(0, len(list(rares)))
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_minimal(self):
a = [
self.headers,
[
'2.12.ribosomal_protein_L11_rplK.gpkg', 'minimal',
'GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC',
'7', '17.07',
'Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales'
],
[
'2.12.ribosomal_protein_L11_rplK.gpkg', 'minimal',
'AGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC',
'9', '18.07',
'Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales'
],
[
'2.12.ribosomal_protein_L11_rplK.gpkg', 'minimal',
'GAAAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC',
'8', '17.57',
'Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales'
],
]
table = "\n".join(["\t".join(x) for x in a] + [''])
e = [
self.output_headers,
[
'reference', '2.12.ribosomal_protein_L11_rplK.gpkg', 'minimal',
'0',
'AGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC',
'9', '18.07',
'Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales'
],
[
'strain', '2.12.ribosomal_protein_L11_rplK.gpkg', 'minimal',
'3',
'GAAAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC',
'8', '17.57',
'Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales'
],
[
'strain', '2.12.ribosomal_protein_L11_rplK.gpkg', 'minimal',
'1',
'GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC',
'7', '17.07',
'Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales'
],
]
exp = "\n".join(["\t".join(x) for x in e] + [''])
output = StringIO()
table_collection = OtuTableCollection()
table_collection.add_otu_table(StringIO(table))
StrainSummariser().summarise_strains(\
table_collection = table_collection,
output_table_io = output)
self.assertEqual(exp, output.getvalue())
def test_nothing_returned(self):
e = [[
'gene', 'sample', 'sequence', 'num_hits', 'coverage', 'taxonomy'
]]
exp = "\n".join(["\t".join(x) for x in e] + [''])
table_collection = OtuTableCollection()
table_collection.add_otu_table(StringIO(exp))
self.assertEqual(0, len(list(table_collection)))
rares = Rarefier().rarefy(table_collection, 0)
self.assertEqual(0, len(list(rares)))
def test_multiple_genes(self):
e = [
['gene', 'sample', 'sequence', 'num_hits', 'coverage', 'taxonomy'],
[
'4.11.ribosomal_protein_L11', 'minimal',
'TTACGTTCACAATTACGTGAAGCTGGTGTTGAGTATAAAGTATACAAAAACACTATGGTA',
'2', '4.88',
'Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus'
],
[
'4.11.ribosomal_protein_L10', 'minimal',
'TTACGTTCACAATTACGTGAAGCTGGTGTTGAGTATAAAGTATACAAAAACACTATGGTT',
'1', '9.76',
'Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales'
],
[
'4.11.ribosomal_protein_L10', 'minimal',
'ATACGTTCACAATTACGTGAAGCTGGTGTTGAGTATAAAGTATACAAAAACACTATGGTT',
'1', '9.76',
'Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales'
]
]
exp = "\n".join(["\t".join(x) for x in e] + [''])
expected = [
['gene', 'sample', 'sequence', 'num_hits', 'coverage', 'taxonomy'],
[
'4.11.ribosomal_protein_L11', 'minimal',
'TTACGTTCACAATTACGTGAAGCTGGTGTTGAGTATAAAGTATACAAAAACACTATGGTA',
2, 4.88,
'Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus'
],
[
'4.11.ribosomal_protein_L10', 'minimal',
'TTACGTTCACAATTACGTGAAGCTGGTGTTGAGTATAAAGTATACAAAAACACTATGGTT',
1, 9.76,
'Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales'
],
[
'4.11.ribosomal_protein_L10', 'minimal',
'ATACGTTCACAATTACGTGAAGCTGGTGTTGAGTATAAAGTATACAAAAACACTATGGTT',
1, 9.76,
'Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales'
]
]
table_collection = OtuTableCollection()
table_collection.add_otu_table(StringIO(exp))
rares = Rarefier().rarefy(
table_collection, 2, random_generator=PredictableRandomGenerator())
self.assertIsInstance(rares, OtuTable)
self.assertEqualOtuTable2(expected, rares)
def test_multiple_samples(self):
metagenome_otu_table = [self.headers,
['4.12.ribosomal_protein_L11_rplK','minimal','GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC','7','17.07','Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales'],
['4.11.ribosomal_protein_L10','another','CCTGCAGGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTG','4','9.76','Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus']
]
metagenomes = "\n".join(["\t".join(x) for x in metagenome_otu_table])
genomes_otu_table = [self.headers,['4.12.ribosomal_protein_L11_rplK','genome','GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC','1','1.02','Root; d__Bacteria; p__Firmicutes; c__Bacilli']
]
genomes = "\n".join(["\t".join(x) for x in genomes_otu_table])
appraiser = Appraiser()
metagenome_collection = OtuTableCollection()
metagenome_collection.add_otu_table(StringIO(metagenomes))
genome_collection = OtuTableCollection()
genome_collection.add_otu_table(StringIO(genomes))
app = appraiser.appraise(genome_otu_table_collection=genome_collection,
metagenome_otu_table_collection=metagenome_collection)
self.assertEqual(2, len(app.appraisal_results))
a = app.appraisal_results[1]
self.assertEqual('minimal', a.metagenome_sample_name)
self.assertEqual(7, a.num_binned)
self.assertEqual(0, a.num_not_found)
a = app.appraisal_results[0]
self.assertEqual('another', a.metagenome_sample_name)
self.assertEqual(0, a.num_binned)
self.assertEqual(4, a.num_not_found)
def test_contamination_near_enough(self):
metagenome_otu_table = [
self.headers,[
'4.12.ribosomal_protein_L11_rplK',
'minimal',
'GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC',
'7','17.07','Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales'],
[
'4.16.ribosomal_protein_S5',
'another',
'GGTACCGGCGTCATCGCCGGTGGCGCGGCACGCGCCATCTTGGAGATGGCCGGCATCCGC',
'8','12.50','Root; d__Bacteria; p__Actinobacteria; c__Actinobacteria']]
metagenomes = "\n".join(["\t".join(x) for x in metagenome_otu_table])
genomes_otu_table = [
self.headers,[
'4.12.ribosomal_protein_L11_rplK',
'genome',
'GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC',
'1','1.02','Root; d__Bacteria; p__Firmicutes; c__Bacilli'],
[
'4.12.ribosomal_protein_L11_rplK',
'genome',
'AGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC', #one base pair different to the one above
'1','1.02','Root; d__Bacteria; p__Firmicutes; c__Bacilli'],
[
'4.16.ribosomal_protein_S5',
'genome',
'GGTACCGGCGTCATCGCCGGTGGGGCGGCACGCGCCATCTTGGAGATGGCCGGCATCCGC',#one base pair different to the one above
'1','1.06','Root; d__Bacteria; p__Actinobacteria; c__Actinobacteria']
]
genomes = "\n".join(["\t".join(x) for x in genomes_otu_table])
appraiser = Appraiser()
metagenome_collection = OtuTableCollection()
metagenome_collection.add_otu_table(StringIO(metagenomes))
genome_collection = OtuTableCollection()
genome_collection.add_otu_table(StringIO(genomes))
app = appraiser.appraise(genome_otu_table_collection=genome_collection,
metagenome_otu_table_collection=metagenome_collection)
self.assertEqual(2, len(app.appraisal_results))
a = app.appraisal_results[0]
self.assertEqual(0, a.num_binned)
self.assertEqual(8, a.num_not_found)
a = app.appraisal_results[1]
self.assertEqual(0, a.num_binned)
self.assertEqual(7, a.num_not_found)
app = appraiser.appraise(genome_otu_table_collection=genome_collection,
metagenome_otu_table_collection=metagenome_collection,
sequence_identity=0.9)
self.assertEqual(2, len(app.appraisal_results))
def compare_res(res): return res.metagenome_sample_name
sorted_results = list(sorted(app.appraisal_results, key=compare_res))
a = sorted_results[0]
self.assertEqual('another', a.metagenome_sample_name)
self.assertEqual(8, a.num_binned)
self.assertEqual(0, a.num_not_found)
a = sorted_results[1]
self.assertEqual(0, a.num_binned)
self.assertEqual(7, a.num_not_found)
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())
def test_using_real_generator(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'],
]
exp = "\n".join(["\t".join(x) for x in e]+[''])
table_collection = OtuTableCollection()
table_collection.add_otu_table(StringIO(exp))
rares = Rarefier().rarefy(table_collection, 2)
self.assertIsInstance(rares, OtuTable)
rares = list(rares)
self.assertEqual(1, len(rares))
self.assertEqual(2, rares[0].count)
def test_cluster_across_samples(self):
e = [['gene','sample','sequence','num_hits','coverage','taxonomy'],
['4.11.ribosomal_protein_L10','minimal','TTACGTTCACAATTACGTGAAGCTGGTGTTGAGTATAAAGTATACAAAAACACT','2','4.88','Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus'],
['4.12.ribosomal_protein_L11_rplK','ma','TTACGTTCACAATTACGTGAAGCTGGTGTTGAGTATAAAGTATACAAAAACACA','4','9.76','Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales']
]
exp = "\n".join(["\t".join(x) for x in e]+[''])
table_collection = OtuTableCollection()
table_collection.add_otu_table(StringIO(exp))
clusters = list(Clusterer().each_cluster(table_collection, 58.5/60))
self.assertEqual(2, len(clusters))
self.assertIsInstance(clusters[0], SampleWiseClusteredOtu)
self.assertEqual(clusters[0].representative_otu, clusters[1].representative_otu)
self.assertEqual('ma', clusters[0].representative_otu.sample_name)
def test_multiple_genes(self):
e = [['gene','sample','sequence','num_hits','coverage','taxonomy'],
['4.11.ribosomal_protein_L11','minimal','TTACGTTCACAATTACGTGAAGCTGGTGTTGAGTATAAAGTATACAAAAACACTATGGTA','2','4.88','Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus'],
['4.11.ribosomal_protein_L10','minimal','TTACGTTCACAATTACGTGAAGCTGGTGTTGAGTATAAAGTATACAAAAACACTATGGTT','1','9.76','Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales'],
['4.11.ribosomal_protein_L10','minimal','ATACGTTCACAATTACGTGAAGCTGGTGTTGAGTATAAAGTATACAAAAACACTATGGTT','1','9.76','Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales']
]
exp = "\n".join(["\t".join(x) for x in e]+[''])
table_collection = OtuTableCollection()
table_collection.add_otu_table(StringIO(exp))
rares = Rarefier().rarefy(table_collection, 2, random_generator=PredictableRandomGenerator())
self.assertIsInstance(rares, OtuTable)
rares = list(rares)
self.assertEqual(3, len(rares))
self.assertEqual([1,1,2], [e.count for e in rares])
def test_cluster_two(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','TTACGTTCACAATTACGTGAAGCTGGTGTTGAGTATAAAGTATACAAAAACACTATGGTT','4','9.76','Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales']
]
exp = "\n".join(["\t".join(x) for x in e]+[''])
table_collection = OtuTableCollection()
table_collection.add_otu_table(StringIO(exp))
clusters = list(Clusterer().each_cluster(table_collection, 0.5))
self.assertEqual(1, len(clusters))
self.assertIsInstance(clusters[0], SampleWiseClusteredOtu)
c = clusters[0]
self.assertEqual(6, c.count)
self.assertEqual(9.76/4*6, c.coverage)
def test_contamination(self):
metagenome_otu_table = [
self.headers,
[
'4.12.ribosomal_protein_L11_rplK', 'minimal',
'GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC',
'7', '17.07',
'Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales'
],
[
'4.16.ribosomal_protein_S5', 'minimal',
'GGTACCGGCGTCATCGCCGGTGGCGCGGCACGCGCCATCTTGGAGATGGCCGGCATCCGC',
'8', '12.50',
'Root; d__Bacteria; p__Actinobacteria; c__Actinobacteria'
]
]
metagenomes = "\n".join(["\t".join(x) for x in metagenome_otu_table])
genomes_otu_table = [
self.headers,
[
'4.12.ribosomal_protein_L11_rplK', 'genome',
'GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC',
'1', '1.02', 'Root; d__Bacteria; p__Firmicutes; c__Bacilli'
],
[
'4.12.ribosomal_protein_L11_rplK',
'genome',
'AGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC', #one base pair different to the one above
'1',
'1.02',
'Root; d__Bacteria; p__Firmicutes; c__Bacilli'
],
[
'4.16.ribosomal_protein_S5', 'genome',
'GGTACCGGCGTCATCGCCGGTGGCGCGGCACGCGCCATCTTGGAGATGGCCGGCATCCGC',
'1', '1.06',
'Root; d__Bacteria; p__Actinobacteria; c__Actinobacteria'
]
]
genomes = "\n".join(["\t".join(x) for x in genomes_otu_table])
appraiser = Appraiser()
metagenome_collection = OtuTableCollection()
metagenome_collection.add_otu_table(StringIO(metagenomes))
genome_collection = OtuTableCollection()
genome_collection.add_otu_table(StringIO(genomes))
app = appraiser.appraise(
genome_otu_table_collection=genome_collection,
metagenome_otu_table_collection=metagenome_collection)
self.assertEqual(1, len(app.appraisal_results))
a = app.appraisal_results[0]
self.assertEqual(8, a.num_binned)
self.assertEqual(7, a.num_not_found)
def test_clusterer_all_cluster_two_samples_some_cluster(self):
# non-As and genome cluster together but are not exactly the same
metagenome_otu_table = [self.headers,
['4.12.ribosomal_protein_L11_rplK','minimal','GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC','7','17.07','Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales'],
['4.12.ribosomal_protein_L11_rplK','minimal','AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA','12','17.07','Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales'],
['4.11.ribosomal_protein_L10','maximal', 'AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA','4','9.76','Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus'],
['4.11.ribosomal_protein_L10','maximal', 'GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATG','1','9.76','Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus']
]
metagenomes = "\n".join(["\t".join(x) for x in metagenome_otu_table])
genomes_otu_table = [self.headers,['4.12.ribosomal_protein_L11_rplK','genome','GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATA','1','1.02','Root; d__Bacteria; p__Firmicutes; c__Bacilli']
]
genomes = "\n".join(["\t".join(x) for x in genomes_otu_table])
appraiser = Appraiser()
metagenome_collection = OtuTableCollection()
metagenome_collection.add_otu_table(StringIO(metagenomes))
genome_collection = OtuTableCollection()
genome_collection.add_otu_table(StringIO(genomes))
app = appraiser.appraise(genome_otu_table_collection=genome_collection,
metagenome_otu_table_collection=metagenome_collection,
sequence_identity=0.7)
self.assertEqual(2, len(app.appraisal_results))
a = app.appraisal_results[1]
self.assertEqual('minimal', a.metagenome_sample_name)
self.assertEqual(7, a.num_binned)
self.assertEqual(12, a.num_not_found)
self.assertEqual(1, len(a.binned_otus))
self.assertEqual(1, len(a.not_found_otus))
self.assertEqual('GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC',
a.binned_otus[0].sequence)
self.assertEqual('minimal',
a.binned_otus[0].sample_name)
self.assertEqual('AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA',
a.not_found_otus[0].sequence)
self.assertEqual('minimal',
a.not_found_otus[0].sample_name)
a = app.appraisal_results[0]
self.assertEqual('maximal', a.metagenome_sample_name)
self.assertEqual(1, a.num_binned)
self.assertEqual(4, a.num_not_found)
self.assertEqual(1, len(a.binned_otus))
self.assertEqual(1, len(a.not_found_otus))
self.assertEqual('GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATG',
a.binned_otus[0].sequence)
self.assertEqual('maximal',
a.binned_otus[0].sample_name)
self.assertEqual('AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA',
a.not_found_otus[0].sequence)
self.assertEqual('maximal',
a.not_found_otus[0].sample_name)
def test_using_real_generator(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'
],
]
exp = "\n".join(["\t".join(x) for x in e] + [''])
table_collection = OtuTableCollection()
table_collection.add_otu_table(StringIO(exp))
rares = Rarefier().rarefy(table_collection, 2)
self.assertIsInstance(rares, OtuTable)
rares = list(rares)
self.assertEqual(1, len(rares))
self.assertEqual(2, rares[0].count)
def test_assembly_input(self):
metagenome_otu_table = [
self.headers,
['4.12.ribosomal_protein_L11_rplK','minimal','GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC','7','17.07','Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales'],
['4.11.ribosomal_protein_L10','minimal','CCTGCAGGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTG','4','9.76','Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus'],
['4.14.ribosomal_protein_L16_L10E_rplP','minimal','CAAAAAAAAAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTG','5','10.76','Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus']]
metagenomes = "\n".join(["\t".join(x) for x in metagenome_otu_table])
assembly_otu_table = [
self.headers,
['4.12.ribosomal_protein_L11_rplK','assembly','GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC','1','1.007','Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales'],
['4.11.ribosomal_protein_L10','assembly','CCTGCAGGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTG','1','1.01','Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus']]
assemblies = "\n".join(["\t".join(x) for x in assembly_otu_table])
genomes_otu_table = [
self.headers,
['4.12.ribosomal_protein_L11_rplK','genome','GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC','1','1.02','Root; d__Bacteria; p__Firmicutes; c__Bacilli']]
genomes = "\n".join(["\t".join(x) for x in genomes_otu_table])
appraiser = Appraiser()
metagenome_collection = OtuTableCollection()
metagenome_collection.add_otu_table(StringIO(metagenomes))
genome_collection = OtuTableCollection()
genome_collection.add_otu_table(StringIO(genomes))
assembly_collection = OtuTableCollection()
assembly_collection.add_otu_table(StringIO(assemblies))
app = appraiser.appraise(genome_otu_table_collection=genome_collection,
metagenome_otu_table_collection=metagenome_collection,
assembly_otu_table_collection=assembly_collection)
self.assertEqual(1, len(app.appraisal_results))
a = app.appraisal_results[0]
self.assertEqual(7, a.num_binned)
self.assertEqual(11, a.num_assembled)
self.assertEqual(5, a.num_not_found)
self.assertEqual('minimal', a.metagenome_sample_name)
self.assertEqual(1, len(a.binned_otus))
self.assertEqual('GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC',
a.binned_otus[0].sequence)
self.assertEqual(2, len(a.assembled_otus))
self.assertEqual(sorted(['GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC',
'CCTGCAGGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTG']),
sorted([o.sequence for o in a.assembled_otus]))
self.assertEqual(1, len(a.not_found_otus))
self.assertEqual('CAAAAAAAAAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTG',
a.not_found_otus[0].sequence)
def test_target_taxonomy(self):
metagenome_otu_table = [
self.headers,
[
'4.12.ribosomal_protein_L11_rplK', 'minimal',
'GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC',
'7', '17.07',
'Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales'
],
[
'4.11.ribosomal_protein_L10', 'minimal',
'CCTGCAGGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTG',
'4', '9.76',
'Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus'
],
[
'4.11.ribosomal_protein_L10', 'minimal',
'CCTGCAGGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTA',
'5', '10.76',
'Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus'
]
]
metagenomes = "\n".join(["\t".join(x) for x in metagenome_otu_table])
table_collection = OtuTableCollection()
table_collection.add_otu_table(StringIO(metagenomes))
self.assertEqual(["minimal\t8.0\t4.75"], [
str(rp)
for rp in Chancer().predict_samples(metagenomes=table_collection,
target_taxonomy=[])
])
self.assertEqual(["minimal\t9.0\t2.5"], [
str(rp) for rp in Chancer().predict_samples(
metagenomes=table_collection,
target_taxonomy=Taxonomy.split_taxonomy(
'Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae'
))
])
def test_print_appraisal(self):
metagenome_otu_table = [self.headers,
['4.12.ribosomal_protein_L11_rplK','minimal','GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC','7','17.07','Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales'],
['4.11.ribosomal_protein_L10','another','CCTGCAGGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTG','4','9.76','Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus']
]
metagenomes = "\n".join(["\t".join(x) for x in metagenome_otu_table])
genomes_otu_table = [self.headers,['4.12.ribosomal_protein_L11_rplK','genome','GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC','1','1.02','Root; d__Bacteria; p__Firmicutes; c__Bacilli']
]
genomes = "\n".join(["\t".join(x) for x in genomes_otu_table])
appraiser = Appraiser()
metagenome_collection = OtuTableCollection()
metagenome_collection.add_otu_table(StringIO(metagenomes))
genome_collection = OtuTableCollection()
genome_collection.add_otu_table(StringIO(genomes))
app = appraiser.appraise(genome_otu_table_collection=genome_collection,
metagenome_otu_table_collection=metagenome_collection)
self.assertEqual(2, len(app.appraisal_results))
a = app.appraisal_results[1]
self.assertEqual('minimal', a.metagenome_sample_name)
self.assertEqual(7, a.num_binned)
self.assertEqual(0, a.num_not_found)
a = app.appraisal_results[0]
self.assertEqual('another', a.metagenome_sample_name)
self.assertEqual(0, a.num_binned)
self.assertEqual(4, a.num_not_found)
to_print = StringIO()
appraiser.print_appraisal(app, True, to_print)
self.assertEqual("sample\tnum_binned\tnum_not_found\tpercent_binned\nanother\t0\t4\t0.0\nminimal\t7\t0\t100.0\ntotal\t7\t4\t63.6\naverage\t3.5\t2.0\t50.0\n", to_print.getvalue())
to_print = StringIO()
found_otu_table_io = StringIO()
not_found_otu_table_io = StringIO()
appraiser.print_appraisal(app, True, to_print,
binned_otu_table_io=found_otu_table_io,
unaccounted_for_otu_table_io=not_found_otu_table_io)
self.assertEqual("\n".join([
"\t".join(self.headers),
"\t".join(['4.12.ribosomal_protein_L11_rplK','minimal','GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC','7','17.07','Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales'])
])+"\n",
found_otu_table_io.getvalue())
self.assertEqual("\n".join([
"\t".join(self.headers),
"\t".join(['4.11.ribosomal_protein_L10','another','CCTGCAGGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTG','4','9.76','Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus'])])+"\n",
not_found_otu_table_io.getvalue())
def test_target_taxonomy(self):
metagenome_otu_table = [
self.headers,
['4.12.ribosomal_protein_L11_rplK','minimal','GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC','7','17.07','Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales'],
['4.11.ribosomal_protein_L10','minimal','CCTGCAGGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTG','4','9.76','Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus'],
['4.11.ribosomal_protein_L10','minimal','CCTGCAGGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTA','5','10.76','Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus']
]
metagenomes = "\n".join(["\t".join(x) for x in metagenome_otu_table])
table_collection = OtuTableCollection()
table_collection.add_otu_table(StringIO(metagenomes))
self.assertEqual(
["minimal\t8.0\t4.75"],
[str(rp) for rp in Chancer().predict_samples(
metagenomes = table_collection,
target_taxonomy = [])]
)
self.assertEqual(
["minimal\t9.0\t2.5"],
[str(rp) for rp in Chancer().predict_samples(
metagenomes = table_collection,
target_taxonomy = Taxonomy.split_taxonomy(
'Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae'))]
)
def test_appraise_plot_real_data(self):
"""Not a real test, just developing the code"""
appraiser = Appraiser()
metagenome_collection = OtuTableCollection()
with open(os.path.join(path_to_data, 'appraise_example2', 'SRR5040536.reads.long_sample_names.otu_table.csv')) as f:
metagenome_collection.add_otu_table(f)
genome_collection = OtuTableCollection()
with open(os.path.join(path_to_data, 'appraise_example2', 'SRR5040536.binned.otu_table.csv')) as f:
genome_collection.add_otu_table(f)
assembly_collection = OtuTableCollection()
with open(os.path.join(path_to_data, 'appraise_example2', 'SRR5040536.assembly.otu_table.csv')) as f:
assembly_collection.add_otu_table(f)
app = appraiser.appraise(genome_otu_table_collection=genome_collection,
metagenome_otu_table_collection=metagenome_collection,
assembly_otu_table_collection=assembly_collection)
with tempfile.NamedTemporaryFile(suffix='.svg',prefix='single_test_appraisal.') as f:
app.plot(
output_svg_base='/tmp/a.svg',#f.name,
cluster_identity = 0.89,
doing_assembly=True,
doing_binning=True
)
def test_contamination(self):
metagenome_otu_table = [
self.headers,[
'4.12.ribosomal_protein_L11_rplK',
'minimal',
'GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC',
'7','17.07','Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales'],
[
'4.16.ribosomal_protein_S5',
'minimal',
'GGTACCGGCGTCATCGCCGGTGGCGCGGCACGCGCCATCTTGGAGATGGCCGGCATCCGC',
'8','12.50','Root; d__Bacteria; p__Actinobacteria; c__Actinobacteria']]
metagenomes = "\n".join(["\t".join(x) for x in metagenome_otu_table])
genomes_otu_table = [
self.headers,[
'4.12.ribosomal_protein_L11_rplK',
'genome',
'GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC',
'1','1.02','Root; d__Bacteria; p__Firmicutes; c__Bacilli'],
[
'4.12.ribosomal_protein_L11_rplK',
'genome',
'AGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC', #one base pair different to the one above
'1','1.02','Root; d__Bacteria; p__Firmicutes; c__Bacilli'],
[
'4.16.ribosomal_protein_S5',
'genome',
'GGTACCGGCGTCATCGCCGGTGGCGCGGCACGCGCCATCTTGGAGATGGCCGGCATCCGC',
'1','1.06','Root; d__Bacteria; p__Actinobacteria; c__Actinobacteria']
]
genomes = "\n".join(["\t".join(x) for x in genomes_otu_table])
appraiser = Appraiser()
metagenome_collection = OtuTableCollection()
metagenome_collection.add_otu_table(StringIO(metagenomes))
genome_collection = OtuTableCollection()
genome_collection.add_otu_table(StringIO(genomes))
app = appraiser.appraise(genome_otu_table_collection=genome_collection,
metagenome_otu_table_collection=metagenome_collection)
self.assertEqual(1, len(app.appraisal_results))
a = app.appraisal_results[0]
self.assertEqual(8, a.num_binned)
self.assertEqual(7, a.num_not_found)
def test_appraise_assembly_imperfectly(self):
metagenome_otu_table = [
self.headers,
[
'4.12.ribosomal_protein_L11_rplK', 'minimal',
'GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC',
'7', '17.07',
'Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales'
],
[
'4.16.ribosomal_protein_S5', 'another',
'GGTACCGGCGTCATCGCCGGTGGCGCGGCACGCGCCATCTTGGAGATGGCCGGCATCCGC',
'8', '12.50',
'Root; d__Bacteria; p__Actinobacteria; c__Actinobacteria'
],
[
'4.16.ribosomal_protein_S5',
'another',
'AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGGCCGGCATCCGC', # way different to the one above
'9',
'17.50',
'Root; d__Bacteria; p__Actinobacteria; c__Actinobacteria'
]
]
metagenomes = "\n".join(["\t".join(x) for x in metagenome_otu_table])
genomes_otu_table = [
self.headers,
[
'4.12.ribosomal_protein_L11_rplK', 'genome',
'GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC',
'1', '1.02', 'Root; d__Bacteria; p__Firmicutes; c__Bacilli'
],
[
'4.12.ribosomal_protein_L11_rplK',
'genome',
'AGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC', #one base pair different to the one above
'1',
'1.02',
'Root; d__Bacteria; p__Firmicutes; c__Bacilli'
],
[
'4.16.ribosomal_protein_S5', 'genome',
'GGTACCGGCGTCATCGCCGGTGGGGCGGCACGCGCCATCTTGGAGATGGCCGGCATCCGC',
'1', '1.06',
'Root; d__Bacteria; p__Actinobacteria; c__Actinobacteria'
]
]
genomes = "\n".join(["\t".join(x) for x in genomes_otu_table])
assemblies_otu_table = [
self.headers,
[
'4.12.ribosomal_protein_L11_rplK', 'assembly',
'GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC',
'1', '1.02', 'Root; d__Bacteria; p__Firmicutes; c__Bacilli'
],
[
'4.12.ribosomal_protein_L11_rplK',
'assembly',
'AGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC', #one base pair different to the one above
'1',
'1.02',
'Root; d__Bacteria; p__Firmicutes; c__Bacilli'
],
[
'4.16.ribosomal_protein_S5', 'assembly',
'GGTACCGGCGTCATCGCCGGTGGGGCGGCACGCGCCATCTTGGAGATGGCCGGCATCCGC',
'1', '1.06',
'Root; d__Bacteria; p__Actinobacteria; c__Actinobacteria'
]
]
assemblies = "\n".join(["\t".join(x) for x in genomes_otu_table])
appraiser = Appraiser()
metagenome_collection = OtuTableCollection()
metagenome_collection.add_otu_table(StringIO(metagenomes))
genome_collection = OtuTableCollection()
genome_collection.add_otu_table(StringIO(genomes))
assembly_collection = OtuTableCollection()
assembly_collection.add_otu_table(StringIO(assemblies))
app = appraiser.appraise(
genome_otu_table_collection=genome_collection,
metagenome_otu_table_collection=metagenome_collection,
assembly_otu_table_collection=assembly_collection)
self.assertEqual(2, len(app.appraisal_results))
res = self._sort_appraisal_results(app.appraisal_results)
a = res[0]
self.assertEqual(0, a.num_binned)
self.assertEqual(0, a.num_assembled)
self.assertEqual(8 + 9, a.num_not_found)
a = res[1]
self.assertEqual(0, a.num_binned)
self.assertEqual(7, a.num_assembled)
self.assertEqual(0, a.num_not_found)
app = appraiser.appraise(
genome_otu_table_collection=genome_collection,
metagenome_otu_table_collection=metagenome_collection,
assembly_otu_table_collection=assembly_collection,
sequence_identity=0.9)
self.assertEqual(2, len(app.appraisal_results))
res = self._sort_appraisal_results(app.appraisal_results)
a = res[0]
self.assertEqual('another', a.metagenome_sample_name)
self.assertEqual(8, a.num_binned)
self.assertEqual(8, a.num_assembled)
self.assertEqual(9, a.num_not_found)
a = res[1]
self.assertEqual(0, a.num_binned)
self.assertEqual(7, a.num_assembled)
self.assertEqual(0, a.num_not_found)
def test_appraise_plot_real_data(self):
"""Not a real test, just developing the code"""
appraiser = Appraiser()
metagenome_collection = OtuTableCollection()
with open(
os.path.join(
path_to_data, 'appraise_example2',
'SRR5040536.reads.long_sample_names.otu_table.csv')) as f:
metagenome_collection.add_otu_table(f)
genome_collection = OtuTableCollection()
with open(
os.path.join(path_to_data, 'appraise_example2',
'SRR5040536.binned.otu_table.csv')) as f:
genome_collection.add_otu_table(f)
assembly_collection = OtuTableCollection()
with open(
os.path.join(path_to_data, 'appraise_example2',
'SRR5040536.assembly.otu_table.csv')) as f:
assembly_collection.add_otu_table(f)
app = appraiser.appraise(
genome_otu_table_collection=genome_collection,
metagenome_otu_table_collection=metagenome_collection,
assembly_otu_table_collection=assembly_collection)
with tempfile.NamedTemporaryFile(suffix='.svg',
prefix='single_test_appraisal.') as f:
app.plot(
output_svg_base='/tmp/a.svg', #f.name,
cluster_identity=0.89,
doing_assembly=True,
doing_binning=True)
def test_assembly_input(self):
metagenome_otu_table = [
self.headers,
[
'4.12.ribosomal_protein_L11_rplK', 'minimal',
'GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC',
'7', '17.07',
'Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales'
],
[
'4.11.ribosomal_protein_L10', 'minimal',
'CCTGCAGGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTG',
'4', '9.76',
'Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus'
],
[
'4.14.ribosomal_protein_L16_L10E_rplP', 'minimal',
'CAAAAAAAAAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTG',
'5', '10.76',
'Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus'
]
]
metagenomes = "\n".join(["\t".join(x) for x in metagenome_otu_table])
assembly_otu_table = [
self.headers,
[
'4.12.ribosomal_protein_L11_rplK', 'assembly',
'GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC',
'1', '1.007',
'Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales'
],
[
'4.11.ribosomal_protein_L10', 'assembly',
'CCTGCAGGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTG',
'1', '1.01',
'Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus'
]
]
assemblies = "\n".join(["\t".join(x) for x in assembly_otu_table])
genomes_otu_table = [
self.headers,
[
'4.12.ribosomal_protein_L11_rplK', 'genome',
'GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC',
'1', '1.02', 'Root; d__Bacteria; p__Firmicutes; c__Bacilli'
]
]
genomes = "\n".join(["\t".join(x) for x in genomes_otu_table])
appraiser = Appraiser()
metagenome_collection = OtuTableCollection()
metagenome_collection.add_otu_table(StringIO(metagenomes))
genome_collection = OtuTableCollection()
genome_collection.add_otu_table(StringIO(genomes))
assembly_collection = OtuTableCollection()
assembly_collection.add_otu_table(StringIO(assemblies))
app = appraiser.appraise(
genome_otu_table_collection=genome_collection,
metagenome_otu_table_collection=metagenome_collection,
assembly_otu_table_collection=assembly_collection)
self.assertEqual(1, len(app.appraisal_results))
a = app.appraisal_results[0]
self.assertEqual(7, a.num_binned)
self.assertEqual(11, a.num_assembled)
self.assertEqual(5, a.num_not_found)
self.assertEqual('minimal', a.metagenome_sample_name)
self.assertEqual(1, len(a.binned_otus))
self.assertEqual(
'GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC',
a.binned_otus[0].sequence)
self.assertEqual(2, len(a.assembled_otus))
self.assertEqual(
sorted([
'GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC',
'CCTGCAGGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTG'
]), sorted([o.sequence for o in a.assembled_otus]))
self.assertEqual(1, len(a.not_found_otus))
self.assertEqual(
'CAAAAAAAAAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTG',
a.not_found_otus[0].sequence)
def test_appraise_assembly_imperfectly(self):
metagenome_otu_table = [
self.headers,[
'4.12.ribosomal_protein_L11_rplK',
'minimal',
'GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC',
'7','17.07','Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales'],
[
'4.16.ribosomal_protein_S5',
'another',
'GGTACCGGCGTCATCGCCGGTGGCGCGGCACGCGCCATCTTGGAGATGGCCGGCATCCGC',
'8','12.50','Root; d__Bacteria; p__Actinobacteria; c__Actinobacteria'],
[
'4.16.ribosomal_protein_S5',
'another',
'AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGGCCGGCATCCGC', # way different to the one above
'9','17.50','Root; d__Bacteria; p__Actinobacteria; c__Actinobacteria']]
metagenomes = "\n".join(["\t".join(x) for x in metagenome_otu_table])
genomes_otu_table = [
self.headers,[
'4.12.ribosomal_protein_L11_rplK',
'genome',
'GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC',
'1','1.02','Root; d__Bacteria; p__Firmicutes; c__Bacilli'],
[
'4.12.ribosomal_protein_L11_rplK',
'genome',
'AGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC', #one base pair different to the one above
'1','1.02','Root; d__Bacteria; p__Firmicutes; c__Bacilli'],
[
'4.16.ribosomal_protein_S5',
'genome',
'GGTACCGGCGTCATCGCCGGTGGGGCGGCACGCGCCATCTTGGAGATGGCCGGCATCCGC',
'1','1.06','Root; d__Bacteria; p__Actinobacteria; c__Actinobacteria']
]
genomes = "\n".join(["\t".join(x) for x in genomes_otu_table])
assemblies_otu_table = [
self.headers,[
'4.12.ribosomal_protein_L11_rplK',
'assembly',
'GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC',
'1','1.02','Root; d__Bacteria; p__Firmicutes; c__Bacilli'],
[
'4.12.ribosomal_protein_L11_rplK',
'assembly',
'AGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC', #one base pair different to the one above
'1','1.02','Root; d__Bacteria; p__Firmicutes; c__Bacilli'],
[
'4.16.ribosomal_protein_S5',
'assembly',
'GGTACCGGCGTCATCGCCGGTGGGGCGGCACGCGCCATCTTGGAGATGGCCGGCATCCGC',
'1','1.06','Root; d__Bacteria; p__Actinobacteria; c__Actinobacteria']
]
assemblies = "\n".join(["\t".join(x) for x in genomes_otu_table])
appraiser = Appraiser()
metagenome_collection = OtuTableCollection()
metagenome_collection.add_otu_table(StringIO(metagenomes))
genome_collection = OtuTableCollection()
genome_collection.add_otu_table(StringIO(genomes))
assembly_collection = OtuTableCollection()
assembly_collection.add_otu_table(StringIO(assemblies))
app = appraiser.appraise(genome_otu_table_collection=genome_collection,
metagenome_otu_table_collection=metagenome_collection,
assembly_otu_table_collection=assembly_collection)
self.assertEqual(2, len(app.appraisal_results))
res = self._sort_appraisal_results(app.appraisal_results)
a = res[0]
self.assertEqual(0, a.num_binned)
self.assertEqual(0, a.num_assembled)
self.assertEqual(8+9, a.num_not_found)
a = res[1]
self.assertEqual(0, a.num_binned)
self.assertEqual(7, a.num_assembled)
self.assertEqual(0, a.num_not_found)
app = appraiser.appraise(genome_otu_table_collection=genome_collection,
metagenome_otu_table_collection=metagenome_collection,
assembly_otu_table_collection=assembly_collection,
sequence_identity=0.9)
self.assertEqual(2, len(app.appraisal_results))
res = self._sort_appraisal_results(app.appraisal_results)
a = res[0]
self.assertEqual('another', a.metagenome_sample_name)
self.assertEqual(8, a.num_binned)
self.assertEqual(8, a.num_assembled)
self.assertEqual(9, a.num_not_found)
a = res[1]
self.assertEqual(0, a.num_binned)
self.assertEqual(7, a.num_assembled)
self.assertEqual(0, a.num_not_found)
