def test_load_file(self):
'''Test _load_file'''
infile = os.path.join(data_dir, 'summary_sample_test_load_file.in.tsv')
with open(infile) as f:
lines = [x.rstrip() for x in f]
dicts = [summary_cluster.SummaryCluster.line2dict(x) for x in lines[1:]]
cluster1 = summary_cluster.SummaryCluster()
cluster1.add_data_dict(dicts[0])
cluster1.add_data_dict(dicts[1])
cluster1.add_data_dict(dicts[2])
cluster1.gather_data()
cluster2 = summary_cluster.SummaryCluster()
cluster2.add_data_dict(dicts[3])
cluster2.add_data_dict(dicts[4])
cluster2.gather_data()
cluster3 = summary_cluster.SummaryCluster()
cluster3.add_data_dict(dicts[5])
cluster3.gather_data()
expected = {
'cluster.n': cluster1,
'cluster.p': cluster2,
'cluster.v': cluster3
}
got = summary_sample.SummarySample._load_file(infile, 90)
self.assertEqual(expected, got)
got = summary_sample.SummarySample._load_file(infile, 90, only_clusters={'cluster.n'})
expected = {'cluster.n': cluster1}
self.assertEqual(expected, got)
def test_gather_data(self):
'''test gather_data'''
lines = [
'ariba_ref1\tref1\t0\t0\t531\t78\tcluster1\t120\t95\t98.42\tctg_name\t279\t24.4\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\tsome free text',
'ariba_ref1\tref1\t1\t0\t531\t78\tcluster1\t120\t100\t98.33\tctg_name\t279\t24.4\t1\tSNP\tn\tI14L\t1\tI14L\tSNP\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnon_coding1:0:0:I14L:.:foo_bar\tspam eggs',
'ariba_ref1\tref1\t0\t0\t531\t78\tcluster1\t120\t100\t98.33\tctg_name\t279\t24.4\t1\tSNP\tn\tA14T\t1\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t40\tT,A\t10,30\tnon_coding1:0:0:A14T:id1:foo_bar\tspam eggs',
'ariba_ref1\tref1\t0\t0\t531\t78\tcluster1\t120\t100\t98.33\tctg_name\t279\t24.4\t1\tSNP\tn\tA14T\t1\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t40\tT,A,G\t20,10,10\tnon_coding1:0:0:A14T:id1:foo_bar\tspam eggs',
]
data_dicts = [
summary_cluster.SummaryCluster.line2dict(x) for x in lines
]
cluster = summary_cluster.SummaryCluster()
for data_dict in data_dicts:
cluster.add_data_dict(data_dict)
cluster.gather_data()
expected_summary = {
'assembled': 'yes',
'match': 'yes',
'ref_seq': 'ref1',
'pct_id': '98.33',
'known_var': 'yes',
'novel_var': 'no',
}
self.assertEqual(expected_summary, cluster.summary)
cluster_vars = [
summary_cluster_variant.SummaryClusterVariant(x)
for x in data_dicts
]
expected_variants = {x for x in cluster_vars if x.has_nonsynon}
self.assertEqual(expected_variants, cluster.variants)
def test_known_noncoding_het_snps(self):
'''test known_noncoding_het_snps'''
lines = [
'ariba_ref1\tref1\t0\t0\t531\t78\tcluster1\t120\t100\t98.33\tctg_name\t279\t24.4\t1\tSNP\tn\tA14T\t1\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnon_coding1:0:0:A14T:id1:foo_bar\tspam eggs',
'ariba_ref1\tref1\t0\t0\t531\t78\tcluster1\t120\t100\t98.33\tctg_name\t279\t24.4\t1\tSNP\tn\tA42T\t1\tA42T\tSNP\t42\t42\tA\t84\t84\tT\t40\tT,A\t10,30\tnon_coding1:0:0:A42T:id1:foo_bar\tspam eggs',
'ariba_ref1\tref1\t0\t0\t531\t78\tcluster1\t120\t100\t98.33\tctg_name\t279\t24.4\t1\tSNP\tn\tA62T\t1\tA62T\tSNP\t62\t62\tA\t84\t84\tA\t40\tA,T\t10,30\tnon_coding1:0:0:A62T:id2:foo_bar\tspam eggs',
'ariba_ref1\tref1\t0\t0\t531\t78\tcluster1\t120\t100\t98.33\tctg_name\t279\t24.4\t1\tSNP\tn\tA82T\t1\tA82T\tSNP\t82\t82\tA\t84\t84\tA\t100\tA,T,G\t10,40,50\tnon_coding1:0:0:A82T:.:foo_bar\tspam eggs'
]
cluster = summary_cluster.SummaryCluster()
for line in lines:
cluster.add_data_dict(
summary_cluster.SummaryCluster.line2dict(line))
got = cluster.known_noncoding_het_snps()
expected = {
'.': {
'A82T': 40.0
},
'id1': {
'A42T': 25.0,
'A14T': 100.0
},
'id2': {
'A62T': 75.0
},
}
self.assertEqual(expected, got)
def test_has_match(self):
'''Test _has_match'''
lines = [
'ariba_refname\trefname\t0\t0\t19\t78\tcluster\t120\t100\t98.33\tctg_name\t279\t24.4\t1\tSNP\tn\tA14T\t1\tA14T\tSYN\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnoncoding1:0:0:A14T:id1:ref has wild type, foo bar\tsome free text',
'ariba_refname\trefname\t0\t0\t19\t78\tcluster\t120\t100\t98.33\tctg_name\t279\t24.4\t0\tSNP\tn\tA14T\t.\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnoncoding1:0:0:A14T:id1:ref has wild type, foo bar\tsome free text',
'ariba_refname\trefname\t0\t1\t19\t78\tcluster\t120\t100\t98.33\tctg_name\t279\t24.4\t1\tSNP\tn\tA14T\t1\tA14T\tSYN\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnoncoding1:0:1:A14T:id1:ref has wild type, foo bar\tsome free text',
'ariba_refname\trefname\t0\t1\t19\t78\tcluster\t120\t100\t98.33\tctg_name\t279\t24.4\t0\tSNP\tn\tA14T\t.\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnoncoding1:0:1:A14T:id1:ref has wild type, foo bar\tsome free text',
'ariba_refname\trefname\t1\t0\t19\t78\tcluster\t120\t100\t98.33\tctg_name\t279\t24.4\t1\tSNP\tp\tA14T\t1\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnoncoding1:1:0:A14T:id1:ref has wild type, foo bar\tsome free text',
'ariba_refname\trefname\t1\t0\t19\t78\tcluster\t120\t100\t98.33\tctg_name\t279\t24.4\t1\tSNP\tp\tA14T\t0\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnoncoding1:1:0:A14T:id1:ref has wild type, foo bar\tsome free text',
'ariba_refname\trefname\t1\t0\t19\t78\tcluster\t120\t100\t98.33\tctg_name\t279\t24.4\t0\tSNP\tp\tA14T\t.\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnoncoding1:1:0:A14T:id1:ref has wild type, foo bar\tsome free text',
'ariba_refname\trefname\t1\t1\t19\t78\tcluster\t120\t100\t98.33\tctg_name\t279\t24.4\t1\tSNP\tp\tA14T\t1\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnoncoding1:1:1:A14T:id1:ref has wild type, foo bar\tsome free text',
'ariba_refname\trefname\t1\t1\t19\t78\tcluster\t120\t100\t98.33\tctg_name\t279\t24.4\t1\tSNP\tp\tA14T\t0\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnoncoding1:1:1:A14T:id1:ref has wild type, foo bar\tsome free text',
'ariba_refname\trefname\t1\t1\t19\t78\tcluster\t120\t100\t98.33\tctg_name\t279\t24.4\t0\tSNP\tp\tA14T\t.\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnoncoding1:1:1:A14T:id1:ref has wild type, foo bar\tsome free text',
]
expected = [
'yes', 'yes', 'yes', 'no', 'yes', 'yes', 'yes', 'yes', 'no', 'no'
]
for i in range(len(lines)):
data_dict = summary_cluster.SummaryCluster.line2dict(lines[i])
cluster = summary_cluster.SummaryCluster()
cluster.add_data_dict(data_dict)
for assembled_summary in ['yes', 'yes_nonunique']:
self.assertEqual(expected[i],
cluster._has_match(assembled_summary))
for assembled_summary in ['no', 'fragmented']:
self.assertEqual('no', cluster._has_match(assembled_summary))
def _load_file(filename, min_pc_id, only_clusters=None):
f = pyfastaq.utils.open_file_read(filename)
clusters = {}
for line in f:
if line.startswith('#'):
if line.rstrip()[1:].split('\t') != report.columns:
pyfastaq.utils.close(f)
raise Error('Error parsing the following line.\n' + line)
continue
data_dict = summary_cluster.SummaryCluster.line2dict(
line, filename=filename)
cluster = data_dict['cluster']
if only_clusters is not None and cluster not in only_clusters:
continue
if cluster not in clusters:
clusters[cluster] = summary_cluster.SummaryCluster(
min_pc_id=min_pc_id)
clusters[cluster].add_data_dict(data_dict)
pyfastaq.utils.close(f)
to_delete = set()
for cluster_name, cluster in clusters.items():
cluster.gather_data()
if cluster.name is None:
to_delete.add(cluster_name)
for name in to_delete:
del clusters[name]
return clusters
def test_non_synon_variants(self):
'''Test non_synon_variants'''
line1 = 'ariba_ref1\tref1\t0\t0\t531\t78\tcluster1\t120\t100\t98.33\tctg_name\t279\t24.4\t1\tSNP\tn\tA14T\t1\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnon_coding1:0:0:A14T:id1:foo_bar\tspam eggs'
line2 = 'ariba_ref1\tref1\t0\t0\t531\t78\tcluster1\t120\t95\t98.42\tctg_name\t279\t24.4\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\tsome free text'
data_dict1 = summary_cluster.SummaryCluster.line2dict(line1)
data_dict2 = summary_cluster.SummaryCluster.line2dict(line2)
cluster = summary_cluster.SummaryCluster()
cluster.add_data_dict(data_dict1)
cluster.add_data_dict(data_dict2)
got = cluster.non_synon_variants()
expected = {('ref1', 'A14T', 'grouped', 'id1')}
self.assertEqual(expected, got)
def test_pc_id_of_longest(self):
'''Test pc_id_of_longest'''
cluster = summary_cluster.SummaryCluster()
self.assertTrue(cluster.name is None)
line1 = 'ariba_refname\trefname\t1\t0\t19\t78\tcluster\t120\t100\t98.33\tctg_name\t279\t24.4\t1\tSNP\tn\tA14T\t1\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnoncoding1:1:0:A14T:id1:ref has wild type, foo bar\tsome free text'
line2 = 'ariba_refname\trefname\t1\t0\t19\t78\tcluster\t120\t119\t98.20\tctg_name2\t279\t24.4\t1\tSNP\tn\tA14T\t1\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnoncoding1:1:0:A14T:id1:ref has wild type, foo bar\tsome free text'
line3 = 'ariba_refname\trefname\t1\t0\t19\t78\tcluster\t120\t114\t98.32\tctg_name3\t279\t24.4\t1\tSNP\tn\tA14T\t1\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnoncoding1:1:0:A14T:id1:ref has wild type, foo bar\tsome free text'
data_dict1 = summary_cluster.SummaryCluster.line2dict(line1)
data_dict2 = summary_cluster.SummaryCluster.line2dict(line2)
data_dict3 = summary_cluster.SummaryCluster.line2dict(line3)
cluster.add_data_dict(data_dict1)
cluster.add_data_dict(data_dict2)
cluster.add_data_dict(data_dict3)
self.assertEqual(98.2, cluster.pc_id_of_longest())
def test_has_any_part_of_ref_assembled(self):
'''Test _has_any_part_of_ref_assembled'''
line1 = 'ariba_refname\trefname\t1\t0\t19\t78\tcluster\t120\t.\t98.33\tctg_name\t279\t24.4\t1\tSNP\tn\tA14T\t1\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnoncoding1:1:0:A14T:id1:ref has wild type, foo bar\tsome free text'
line2 = 'ariba_refname\trefname\t1\t0\t19\t78\tcluster\t120\t0\t98.33\tctg_name\t279\t24.4\t1\tSNP\tn\tA14T\t1\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnoncoding1:1:0:A14T:id1:ref has wild type, foo bar\tsome free text'
line3 = 'ariba_refname\trefname\t1\t0\t19\t78\tcluster\t120\t100\t98.33\tctg_name\t279\t24.4\t1\tSNP\tn\tA14T\t1\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnoncoding1:1:0:A14T:id1:ref has wild type, foo bar\tsome free text'
data_dict1 = summary_cluster.SummaryCluster.line2dict(line1)
data_dict2 = summary_cluster.SummaryCluster.line2dict(line2)
data_dict3 = summary_cluster.SummaryCluster.line2dict(line3)
cluster = summary_cluster.SummaryCluster()
cluster.add_data_dict(data_dict1)
self.assertFalse(cluster._has_any_part_of_ref_assembled())
cluster.add_data_dict(data_dict2)
self.assertFalse(cluster._has_any_part_of_ref_assembled())
cluster.add_data_dict(data_dict3)
self.assertTrue(cluster._has_any_part_of_ref_assembled())
def test_add_data_dict(self):
'''Test add_data_dict'''
cluster = summary_cluster.SummaryCluster()
self.assertTrue(cluster.name is None)
line1 = 'ariba_refname1\trefname\t1\t0\t19\t78\tcluster\t120\t120\t98.33\tctg_name\t279\t24.4\t1\tSNP\tn\tA14T\t1\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnoncoding1:1:0:A14T:id1:ref has wild type, foo bar\tsome free text'
line2 = 'ariba_refname1\trefname\t1\t0\t19\t78\tcluster2\t120\t120\t98.33\tctg_name\t279\t24.4\t1\tSNP\tn\tA14T\t1\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnoncoding1:1:0:A14T:id2:ref has wild type, foo bar\tsome free text'
line3 = 'ariba_refname2\trefname2\t1\t0\t19\t78\tcluster\t120\t120\t98.33\tctg_name\t279\t24.4\t1\tSNP\tn\tA14T\t1\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnoncoding1:1:0:A14T:id3:ref has wild type, foo bar\tsome free text'
data_dict1 = summary_cluster.SummaryCluster.line2dict(line1)
data_dict2 = summary_cluster.SummaryCluster.line2dict(line2)
data_dict3 = summary_cluster.SummaryCluster.line2dict(line3)
cluster.add_data_dict(data_dict1)
self.assertEqual(cluster.name, data_dict1['cluster'])
self.assertEqual(cluster.data, [data_dict1])
with self.assertRaises(summary_cluster.Error):
cluster.add_data_dict(data_dict2)
with self.assertRaises(summary_cluster.Error):
cluster.add_data_dict(data_dict3)
def test_has_any_known_variant(self):
lines = [
'ariba_refname\trefname\t0\t0\t19\t78\tcluster\t120\t100\t98.33\tctg_name\t279\t24.4\t1\tSNP\tn\tA14T\t1\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnoncoding1:0:0:A14T:id1:ref has wild type, foo bar\tsome free text',
'ariba_refname\trefname\t0\t0\t19\t78\tcluster\t120\t100\t98.33\tctg_name\t279\t24.4\t1\tSNP\tn\tA14T\t0\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnoncoding1:0:0:A14T:id1:ref has wild type, foo bar\tsome free text',
'ariba_refname\trefname\t0\t0\t19\t78\tcluster\t120\t100\t98.33\tctg_name\t279\t24.4\t0\tSNP\tn\t.\t.\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnoncoding1:0:0:A14T:id1:ref has wild type, foo bar\tsome free text',
'ariba_refname\trefname\t1\t0\t528\t2814\tcluster\t1188\t1009\t90.49\tctg_name\t2470\t141.8\t0\t.\tp\t.\t0\t.\tMULTIPLE\t594\t594\tC;T\t1195\t1195\t.;C\t207;204\t.;.\t207;204\t.\t.',
'ariba_refname\trefname\t1\t0\t528\t2814\tcluster\t1188\t1009\t90.49\tctg_name\t2470\t141.8\t0\t.\tp\t.\t0\t.\tINDELS\t594\t594\tC;T\t1195\t1195\t.;C\t207;204\t.;.\t207;204\t.\t.',
'ariba_23S.rDNA_WHO_F_01358c\t23S.rDNA_WHO_F_01358c\t0\t1\t659\t4168\t23S\t2890\t2890\t99.86\t23S.scaffold.1\t3628\t344.0\t1\tSNP\tn\tC2597T\t0\t.\t.\t2597\t2597\tC\t2928\t2928\tC\t410\tC,T\t70,30\t23S.rDNA_WHO_F_01358c:0:1:C2597T:.:E coli C2611T\t.',
]
expected = ['yes', 'no', 'no', 'no', 'no', 'het']
assert len(lines) == len(expected)
for i in range(len(lines)):
data_dict = summary_cluster.SummaryCluster.line2dict(lines[i])
cluster = summary_cluster.SummaryCluster()
cluster.add_data_dict(data_dict)
self.assertEqual(expected[i], cluster._has_any_known_variant())
def test_column_summary_data(self):
'''Test column_summary_data'''
line1 = 'ariba_ref1\tref1\t0\t0\t531\t78\tcluster1\t120\t100\t98.33\tctg_name\t279\t24.4\t1\tSNP\tn\tA14T\t1\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnon_coding1:n:A14T:id1:foo_bar\tspam eggs'
line2 = 'ariba_ref1\tref1\t0\t0\t531\t78\tcluster1\t120\t95\t98.42\tctg_name\t279\t24.4\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\tsome free text'
data_dict1 = summary_cluster.SummaryCluster.line2dict(line1)
data_dict2 = summary_cluster.SummaryCluster.line2dict(line2)
cluster = summary_cluster.SummaryCluster()
cluster.add_data_dict(data_dict1)
cluster.add_data_dict(data_dict2)
expected = {
'assembled': 'yes',
'match': 'yes',
'ref_seq': 'ref1',
'novel_var': 'no',
'known_var': 'yes',
'pct_id': '98.33',
}
got = cluster.column_summary_data()
self.assertEqual(expected, got)
def test_has_any_nonsynonymous(self):
'''Test _has_any_nonsynonymous'''
lines = [
'ariba_refname\trefname\t0\t0\t19\t78\tcluster\t120\t100\t98.33\tctg_name\t279\t24.4\t1\tSNP\tn\tA14T\t1\tA14T\tSYN\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnoncoding1:0:0:A14T:N_ref has wild type, foo bar\tsome free text',
'ariba_refname\trefname\t0\t0\t19\t78\tcluster\t120\t100\t98.33\tctg_name\t279\t24.4\t1\tSNP\tn\tA14T\t1\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnoncoding1:0:0:A14T:id1:ref has wild type, foo bar\tsome free text',
'ariba_refname\trefname\t0\t0\t19\t78\tcluster\t120\t100\t98.33\tctg_name\t279\t24.4\t1\tSNP\tn\tA14T\t0\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnoncoding1:0:0:A14T:id1:ref has wild type, foo bar\tsome free text',
'ariba_refname\trefname\t0\t0\t19\t78\tcluster\t120\t100\t98.33\tctg_name\t279\t24.4\t0\tSNP\tn\t.\t.\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnoncoding1:0:0:A14T:id1:ref has wild type, foo bar\tsome free text',
'ariba_refname\trefname\t0\t0\t19\t78\tcluster\t120\t100\t98.33\tctg_name\t279\t24.4\t0\tSNP\tn\t.\t.\t.\tMULTIPLE\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnoncoding1:0:0:A14T:id1:ref has wild type, foo bar\tsome free text',
'ariba_23S.rDNA_WHO_F_01358c\t23S.rDNA_WHO_F_01358c\t0\t1\t659\t4168\t23S\t2890\t2890\t99.86\t23S.scaffold.1\t3628\t344.0\t0\tHET\t.\t.\t.\t.\t.\t2597\t2597\tC\t2928\t2928\tC\t410\tC,T\t70,30\t.\t.',
'ariba_ref1\tref1\t0\t0\t531\t78\tcluster1\t120\t100\t98.33\tctg_name\t279\t24.4\t1\tSNP\tn\tA62T\t1\tA62T\tSNP\t62\t62\tA\t84\t84\tA\t40\tA,T\t10,30\tnon_coding1:0:0:A62T:id2:foo_bar\tspam eggs',
]
expected = ['no', 'yes', 'no', 'yes', 'yes', 'het', 'het']
assert len(lines) == len(expected)
for i in range(len(lines)):
data_dict = summary_cluster.SummaryCluster.line2dict(lines[i])
cluster = summary_cluster.SummaryCluster()
cluster.add_data_dict(data_dict)
self.assertEqual(expected[i], cluster._has_any_nonsynonymous())
def test_has_var_groups(self):
'''Test has_var_groups'''
lines = [
'ariba_refname\trefname\t0\t0\t19\t78\tcluster\t120\t100\t98.33\tctg_name\t279\t24.4\t1\tSNP\tn\tA14T\t1\tA14T\tSYN\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnoncoding1:0:0:A14T:id1:ref has wild type, foo bar\tsome free text',
'ariba_refname\trefname\t0\t0\t19\t78\tcluster\t120\t100\t98.33\tctg_name\t279\t24.4\t0\tSNP\tn\tA14T\t.\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnoncoding1:0:0:A14T:id2:ref has wild type, foo bar\tsome free text',
'ariba_refname\trefname\t1\t0\t19\t78\tcluster\t120\t100\t98.33\tctg_name\t279\t24.4\t1\tSNP\tp\tA14T\t1\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnoncoding1:1:0:A14T:id3:ref has wild type, foo bar\tsome free text',
'ariba_refname\trefname\t1\t0\t19\t78\tcluster\t120\t100\t98.33\tctg_name\t279\t24.4\t1\tSNP\tp\tA14T\t0\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnoncoding1:1:0:A14T:id4:ref has wild type, foo bar\tsome free text',
'ariba_refname\trefname\t1\t0\t19\t78\tcluster\t120\t100\t98.33\tctg_name\t279\t24.4\t0\tSNP\tp\tA14T\t.\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnoncoding1:1:0:A14T:id5:ref has wild type, foo bar\tsome free text',
'ariba_refname\trefname\t1\t1\t19\t78\tcluster\t120\t100\t98.33\tctg_name\t279\t24.4\t1\tSNP\tp\tA14T\t1\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnoncoding1:1:1:A14T:id6:ref has wild type, foo bar\tsome free text',
'ariba_refname\trefname\t1\t1\t19\t78\tcluster\t120\t100\t98.33\tctg_name\t279\t24.4\t1\tSNP\tp\tA14T\t0\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnoncoding1:1:1:A14T:id7:ref has wild type, foo bar\tsome free text',
'ariba_refname\trefname\t1\t1\t19\t78\tcluster\t120\t100\t98.33\tctg_name\t279\t24.4\t0\tSNP\tp\tA14T\t.\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnoncoding1:1:1:A14T:id7:ref has wild type, foo bar\tsome free text',
]
dicts = [
summary_cluster.SummaryCluster.line2dict(line) for line in lines
]
cluster = summary_cluster.SummaryCluster()
for d in dicts:
cluster.add_data_dict(d)
got = cluster.has_var_groups()
expected = {'id1', 'id3', 'id6'}
self.assertEqual(expected, got)
def test_to_cluster_summary_number(self):
'''Test _to_cluster_summary_assembled'''
line = 'ariba_refname\trefname\t0\t0\t19\t78\tcluster\t120\t100\t98.33\tctg_name\t279\t24.4\t1\tSNP\tn\tA14T\t1\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnoncoding1:0:0:A14T:id1:ref has wild type, foo bar\tsome free text'
data_dict = summary_cluster.SummaryCluster.line2dict(line)
tests = [
('0', 0, 'partial'),
('0', 64, 'no'),
('0', 1024, 'no'),
('0', 1, 'fragmented'),
('0', 3, 'yes_nonunique'),
('0', 19, 'yes'),
('0', 23, 'yes_nonunique'),
('0', 51, 'yes_nonunique'),
('0', 147, 'yes_nonunique'),
('0', 275, 'yes_nonunique'),
('1', 0, 'partial'),
('1', 64, 'no'),
('1', 1024, 'no'),
('1', 1, 'fragmented'),
('1', 11, 'yes_nonunique'),
('1', 27, 'yes'),
('1', 29, 'fragmented'),
('1', 59, 'yes_nonunique'),
('1', 155, 'yes_nonunique'),
('1', 283, 'yes_nonunique'),
]
for gene, f, expected in tests:
cluster = summary_cluster.SummaryCluster()
data_dict['gene'] = gene
data_dict['flag'] = flag.Flag(f)
cluster.add_data_dict(data_dict)
self.assertEqual(expected, cluster._to_cluster_summary_assembled())
if expected == 'partial':
original_number = cluster.data[0]['ref_base_assembled']
cluster.data[0]['ref_base_assembled'] = 0
self.assertEqual('no', cluster._to_cluster_summary_assembled())
cluster.data[0]['ref_base_assembled'] = original_number
