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_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_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_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_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_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_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_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_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)
