def test_read(self):
self.cn.write()
test_cn = CopyNumberFile(self.cn.path, 'test5', self.test_markers)
test_cn.read()
genome_1_truth = {'unq': {'PFAM_1': None, 'TIGR_1': None
},
'muq': {'PFAM_2': None},
'mul': {},
'mis': {'PFAM_3': None, 'TIGR_2': None}
}
genome_2_truth = {'unq': {'PFAM_2': None},
'muq': {'TIGR_1': None, 'TIGR_2': None},
'mul': {'PFAM_1': None, 'PFAM_3': None},
'mis': {}}
self.assertDictEqual(genome_1_truth, test_cn.genomes['genome_1'])
self.assertDictEqual(genome_2_truth, test_cn.genomes['genome_2'])
def test__merge_hit_files(self):
pfam_th = TopHitPfamFile(os.path.join(self.dir_tmp), 'genome_1')
pfam_th.add_hit('gene_a', 'PFAM_1', 0.05, 100)
pfam_th.add_hit('gene_b', 'PFAM_2', 0.05, 200)
pfam_th.add_hit('gene_c', 'PFAM_2', 0.05, 100)
tigr_th = TopHitTigrFile(os.path.join(self.dir_tmp), 'genome_1')
tigr_th.add_hit('gene_x', 'TIGR_1', 0.05, 100)
expected = {'TIGR_1': [Hit('gene_x', 'TIGR_1', 0.05, 100)],
'PFAM_1': [Hit('gene_a', 'PFAM_1', 0.05, 100)],
'PFAM_2': [Hit('gene_b', 'PFAM_2', 0.05, 200),
Hit('gene_c', 'PFAM_2', 0.05, 100)]}
self.assertDictEqual(expected, CopyNumberFile._merge_hit_files(pfam_th, tigr_th))
def setUp(self):
self.dir_tmp = tempfile.mkdtemp(prefix='gtdbtk_tmp_')
# Build a test set of markers
self.test_markers = {
"PFAM": ["PFAM_1.hmm", "PFAM_2.hmm", "PFAM_3.hmm"],
"TIGRFAM": ["TIGR_1.HMM", "TIGR_2.HMM"]
}
# Build the copy number file
self.cn_path = os.path.join(self.dir_tmp, 'cn.tsv')
self.cn = CopyNumberFile(self.cn_path, 'test5', self.test_markers)
# Store the hit files
self.pfam_th = dict()
self.tigr_th = dict()
self.faa = dict()
# Test case for genome_1
"""
Single Copy: PFAM_1, TIGR_1
Multi-Unique: PFAM_2
Multi-Copy: None
Missing: PFAM_3, TIGR_2
"""
self.pfam_th['genome_1'] = TopHitPfamFile(os.path.join(self.dir_tmp),
'genome_1')
self.pfam_th['genome_1'].add_hit('gene_a', 'PFAM_1', 0.05, 100)
self.pfam_th['genome_1'].add_hit('gene_b', 'PFAM_2', 0.05, 200)
self.pfam_th['genome_1'].add_hit('gene_c', 'PFAM_2', 0.05, 100)
self.pfam_th['genome_1'].write()
self.tigr_th['genome_1'] = TopHitTigrFile(os.path.join(self.dir_tmp),
'genome_1')
self.tigr_th['genome_1'].add_hit('gene_x', 'TIGR_1', 0.05, 100)
self.faa['genome_1'] = os.path.join(self.dir_tmp, 'genome_1.faa')
with open(self.faa['genome_1'], 'w') as fh:
fh.write('>gene_a\n')
fh.write('VVVVVV\n')
fh.write('>gene_b\n')
fh.write('AAVVPP\n')
fh.write('>gene_c\n')
fh.write('AAVVPP\n')
fh.write('>gene_x\n')
fh.write('AAAAAA\n')
# Test case for genome_2
"""
Single Copy: PFAM_2
Multi-Unique: TIGR_1, TIGR_2
Multi-Copy: PFAM_1, PFAM_3
Missing: None
"""
self.pfam_th['genome_2'] = TopHitPfamFile(os.path.join(self.dir_tmp),
'genome_2')
self.pfam_th['genome_2'].add_hit('gene_a', 'PFAM_2', 0.05, 100)
self.pfam_th['genome_2'].add_hit('gene_w', 'PFAM_1', 0.05, 100)
self.pfam_th['genome_2'].add_hit('gene_z', 'PFAM_1', 0.05, 100)
self.pfam_th['genome_2'].add_hit('gene_y', 'PFAM_3', 0.05, 100)
self.pfam_th['genome_2'].add_hit('gene_x', 'PFAM_3', 0.05, 100)
self.pfam_th['genome_2'].write()
self.tigr_th['genome_2'] = TopHitTigrFile(os.path.join(self.dir_tmp),
'genome_2')
self.tigr_th['genome_2'].add_hit('gene_w', 'TIGR_1', 0.05, 100)
self.tigr_th['genome_2'].add_hit('gene_x', 'TIGR_1', 0.05, 200)
self.tigr_th['genome_2'].add_hit('gene_y', 'TIGR_2', 0.01, 100)
self.tigr_th['genome_2'].add_hit('gene_z', 'TIGR_2', 0.05, 100)
self.faa['genome_2'] = os.path.join(self.dir_tmp, 'genome_2.faa')
with open(self.faa['genome_2'], 'w') as fh:
fh.write('>gene_a\n')
fh.write('VVVVVV\n')
fh.write('>gene_w\n')
fh.write('AAAVVV\n')
fh.write('>gene_x\n')
fh.write('AAAVVV\n')
fh.write('>gene_y\n')
fh.write('VVVAAA\n')
fh.write('>gene_z\n')
fh.write('VVVAAA\n')
# Add the genomes
for gid in self.faa:
self.cn.add_genome(gid,
self.faa[gid],
pfam_th=self.pfam_th[gid],
tigr_th=self.tigr_th[gid])
class TestCopyNumberFile(unittest.TestCase):
def setUp(self):
self.dir_tmp = tempfile.mkdtemp(prefix='gtdbtk_tmp_')
# Build a test set of markers
self.test_markers = {
"PFAM": ["PFAM_1.hmm", "PFAM_2.hmm", "PFAM_3.hmm"],
"TIGRFAM": ["TIGR_1.HMM", "TIGR_2.HMM"]
}
# Build the copy number file
self.cn_path = os.path.join(self.dir_tmp, 'cn.tsv')
self.cn = CopyNumberFile(self.cn_path, 'test5', self.test_markers)
# Store the hit files
self.pfam_th = dict()
self.tigr_th = dict()
self.faa = dict()
# Test case for genome_1
"""
Single Copy: PFAM_1, TIGR_1
Multi-Unique: PFAM_2
Multi-Copy: None
Missing: PFAM_3, TIGR_2
"""
self.pfam_th['genome_1'] = TopHitPfamFile(os.path.join(self.dir_tmp),
'genome_1')
self.pfam_th['genome_1'].add_hit('gene_a', 'PFAM_1', 0.05, 100)
self.pfam_th['genome_1'].add_hit('gene_b', 'PFAM_2', 0.05, 200)
self.pfam_th['genome_1'].add_hit('gene_c', 'PFAM_2', 0.05, 100)
self.pfam_th['genome_1'].write()
self.tigr_th['genome_1'] = TopHitTigrFile(os.path.join(self.dir_tmp),
'genome_1')
self.tigr_th['genome_1'].add_hit('gene_x', 'TIGR_1', 0.05, 100)
self.faa['genome_1'] = os.path.join(self.dir_tmp, 'genome_1.faa')
with open(self.faa['genome_1'], 'w') as fh:
fh.write('>gene_a\n')
fh.write('VVVVVV\n')
fh.write('>gene_b\n')
fh.write('AAVVPP\n')
fh.write('>gene_c\n')
fh.write('AAVVPP\n')
fh.write('>gene_x\n')
fh.write('AAAAAA\n')
# Test case for genome_2
"""
Single Copy: PFAM_2
Multi-Unique: TIGR_1, TIGR_2
Multi-Copy: PFAM_1, PFAM_3
Missing: None
"""
self.pfam_th['genome_2'] = TopHitPfamFile(os.path.join(self.dir_tmp),
'genome_2')
self.pfam_th['genome_2'].add_hit('gene_a', 'PFAM_2', 0.05, 100)
self.pfam_th['genome_2'].add_hit('gene_w', 'PFAM_1', 0.05, 100)
self.pfam_th['genome_2'].add_hit('gene_z', 'PFAM_1', 0.05, 100)
self.pfam_th['genome_2'].add_hit('gene_y', 'PFAM_3', 0.05, 100)
self.pfam_th['genome_2'].add_hit('gene_x', 'PFAM_3', 0.05, 100)
self.pfam_th['genome_2'].write()
self.tigr_th['genome_2'] = TopHitTigrFile(os.path.join(self.dir_tmp),
'genome_2')
self.tigr_th['genome_2'].add_hit('gene_w', 'TIGR_1', 0.05, 100)
self.tigr_th['genome_2'].add_hit('gene_x', 'TIGR_1', 0.05, 200)
self.tigr_th['genome_2'].add_hit('gene_y', 'TIGR_2', 0.01, 100)
self.tigr_th['genome_2'].add_hit('gene_z', 'TIGR_2', 0.05, 100)
self.faa['genome_2'] = os.path.join(self.dir_tmp, 'genome_2.faa')
with open(self.faa['genome_2'], 'w') as fh:
fh.write('>gene_a\n')
fh.write('VVVVVV\n')
fh.write('>gene_w\n')
fh.write('AAAVVV\n')
fh.write('>gene_x\n')
fh.write('AAAVVV\n')
fh.write('>gene_y\n')
fh.write('VVVAAA\n')
fh.write('>gene_z\n')
fh.write('VVVAAA\n')
# Add the genomes
for gid in self.faa:
self.cn.add_genome(gid,
self.faa[gid],
pfam_th=self.pfam_th[gid],
tigr_th=self.tigr_th[gid])
def tearDown(self):
self.cn = None
self.pfam_th = None
self.tigr_th = None
shutil.rmtree(self.dir_tmp)
def test_add_genome(self):
genome_1_truth = {
'unq': {
'PFAM_1': {
'hit': Hit('gene_a', 'PFAM_1', 0.05, 100),
'seq': 'VVVVVV'
},
'TIGR_1': {
'hit': Hit('gene_x', 'TIGR_1', 0.05, 100),
'seq': 'AAAAAA'
}
},
'muq': {
'PFAM_2': {
'hit': Hit('gene_b', 'PFAM_2', 0.05, 200),
'seq': 'AAVVPP'
}
},
'mul': {},
'mis': {
'PFAM_3': None,
'TIGR_2': None
}
}
genome_2_truth = {
'unq': {
'PFAM_2': {
'hit': Hit('gene_a', 'PFAM_2', 0.05, 100),
'seq': 'VVVVVV'
}
},
'muq': {
'TIGR_1': {
'hit': Hit('gene_x', 'TIGR_1', 0.05, 200),
'seq': 'AAAVVV'
},
'TIGR_2': {
'hit': Hit('gene_y', 'TIGR_2', 0.01, 100),
'seq': 'VVVAAA'
}
},
'mul': {
'PFAM_1': None,
'PFAM_3': None
},
'mis': {}
}
self.assertDictEqual(genome_1_truth, self.cn.genomes['genome_1'])
self.assertDictEqual(genome_2_truth, self.cn.genomes['genome_2'])
def test__extract_marker_names(self):
true = {'PFAM_1', 'PFAM_2', 'PFAM_3', 'TIGR_1', 'TIGR_2'}
self.assertSetEqual(
true, CopyNumberFile._extract_marker_names(self.test_markers))
def test__merge_hit_files(self):
pfam_th = TopHitPfamFile(os.path.join(self.dir_tmp), 'genome_1')
pfam_th.add_hit('gene_a', 'PFAM_1', 0.05, 100)
pfam_th.add_hit('gene_b', 'PFAM_2', 0.05, 200)
pfam_th.add_hit('gene_c', 'PFAM_2', 0.05, 100)
tigr_th = TopHitTigrFile(os.path.join(self.dir_tmp), 'genome_1')
tigr_th.add_hit('gene_x', 'TIGR_1', 0.05, 100)
expected = {
'TIGR_1': [Hit('gene_x', 'TIGR_1', 0.05, 100)],
'PFAM_1': [Hit('gene_a', 'PFAM_1', 0.05, 100)],
'PFAM_2': [
Hit('gene_b', 'PFAM_2', 0.05, 200),
Hit('gene_c', 'PFAM_2', 0.05, 100)
]
}
self.assertDictEqual(expected,
CopyNumberFile._merge_hit_files(pfam_th, tigr_th))
def test_get_single_copy_hits(self):
g1_expected = {
'PFAM_1': {
'hit': Hit('gene_a', 'PFAM_1', 0.05, 100),
'seq': 'VVVVVV'
},
'TIGR_1': {
'hit': Hit('gene_x', 'TIGR_1', 0.05, 100),
'seq': 'AAAAAA'
},
'PFAM_2': {
'hit': Hit('gene_b', 'PFAM_2', 0.05, 200),
'seq': 'AAVVPP'
}
}
g2_expected = {
'PFAM_2': {
'hit': Hit('gene_a', 'PFAM_2', 0.05, 100),
'seq': 'VVVVVV'
},
'TIGR_1': {
'hit': Hit('gene_x', 'TIGR_1', 0.05, 200),
'seq': 'AAAVVV'
},
'TIGR_2': {
'hit': Hit('gene_y', 'TIGR_2', 0.01, 100),
'seq': 'VVVAAA'
}
}
self.assertDictEqual(g1_expected,
self.cn.get_single_copy_hits('genome_1'))
self.assertDictEqual(g2_expected,
self.cn.get_single_copy_hits('genome_2'))
def test_write(self):
self.cn.write()
with open(self.cn.path) as fh:
self.assertEqual(
'name\tnumber_unique_genes\tnumber_multiple_genes\t'
'number_multiple_unique_genes\tnumber_missing_genes\t'
'list_unique_genes\tlist_multiple_genes\t'
'list_multiple_unique_genes\tlist_missing_genes\n',
fh.readline())
self.assertEqual(
'genome_1\t2\t0\t1\t2\t'
'PFAM_1,TIGR_1\t\tPFAM_2\tPFAM_3,TIGR_2\n', fh.readline())
self.assertEqual(
'genome_2\t1\t2\t2\t0\t'
'PFAM_2\tPFAM_1,PFAM_3\tTIGR_1,TIGR_2\t\n', fh.readline())
def test_read(self):
self.cn.write()
test_cn = CopyNumberFile(self.cn.path, 'test5', self.test_markers)
test_cn.read()
genome_1_truth = {
'unq': {
'PFAM_1': None,
'TIGR_1': None
},
'muq': {
'PFAM_2': None
},
'mul': {},
'mis': {
'PFAM_3': None,
'TIGR_2': None
}
}
genome_2_truth = {
'unq': {
'PFAM_2': None
},
'muq': {
'TIGR_1': None,
'TIGR_2': None
},
'mul': {
'PFAM_1': None,
'PFAM_3': None
},
'mis': {}
}
self.assertDictEqual(genome_1_truth, test_cn.genomes['genome_1'])
self.assertDictEqual(genome_2_truth, test_cn.genomes['genome_2'])
def test__extract_marker_names(self):
true = {'PFAM_1', 'PFAM_2', 'PFAM_3', 'TIGR_1', 'TIGR_2'}
self.assertSetEqual(
true, CopyNumberFile._extract_marker_names(self.test_markers))