def test_build_tree(self):
taxid_data_fp = get_data_path('taxid_data.txt')
taxid_data = taxidtool.parse_taxid_data(taxid_data_fp)
sequences_input_fp = get_data_path('sequences.fasta')
inclusion_roots = ["6"]
exclusion_roots = ["20"]
results = taxidtool.build_tree(taxid_data, sequences_input_fp,
inclusion_roots, exclusion_roots)
self.assertEqual(set(results.keys()), {'6', '16', '18', '22'})
def test_build_tree(self):
taxid_data_fp = get_data_path('taxid_data.txt')
taxid_data = taxidtool.parse_taxid_data(taxid_data_fp)
sequences_input_fp = get_data_path('sequences.fasta')
inclusion_roots = ["6"]
exclusion_roots = ["20"]
results = taxidtool.build_tree(taxid_data,
sequences_input_fp,
inclusion_roots,
exclusion_roots)
self.assertEqual(set(results.keys()), {'6', '16', '18', '22'})
def test_write_taxid_data(self):
nodes_fp = get_data_path('nodes.dmp')
names_fp = get_data_path('names.dmp')
gi_taxid_nucl_fp = get_data_path("gi_taxid_nucl.dmp")
results = taxidtool.build_taxid_data(nodes_fp, names_fp,
gi_taxid_nucl_fp)
with tempfile.NamedTemporaryFile() as fh:
taxidtool.write_taxid_data(results, fh.name)
data = taxidtool.parse_taxid_data(fh.name)
with tempfile.NamedTemporaryFile() as fh2:
taxidtool.write_taxid_data(data, fh2.name)
data2 = taxidtool.parse_taxid_data(fh2.name)
self.assertEqual(set(data.keys()), set(data2.keys()))
def test_write_taxid_data(self):
nodes_fp = get_data_path('nodes.dmp')
names_fp = get_data_path('names.dmp')
gi_taxid_nucl_fp = get_data_path("gi_taxid_nucl.dmp")
results = taxidtool.build_taxid_data(nodes_fp,
names_fp,
gi_taxid_nucl_fp)
with tempfile.NamedTemporaryFile() as fh:
taxidtool.write_taxid_data(results, fh.name)
data = taxidtool.parse_taxid_data(fh.name)
with tempfile.NamedTemporaryFile() as fh2:
taxidtool.write_taxid_data(data, fh2.name)
data2 = taxidtool.parse_taxid_data(fh2.name)
self.assertEqual(set(data.keys()), set(data2.keys()))
def test_build_taxid_data(self):
nodes_fp = get_data_path('nodes.dmp')
names_fp = get_data_path('names.dmp')
gi_taxid_nucl_fp = get_data_path("gi_taxid_nucl.dmp")
results = taxidtool.build_taxid_data(nodes_fp, names_fp,
gi_taxid_nucl_fp)
for taxid, record in results.items():
self.assertEqual(record.taxid, taxid)
self.assertEqual(record.sci_name, "Node%s" % taxid)
for gi in record.assoc_gis:
self.assertTrue(gi.startswith(taxid))
self.assertEqual(results['23'].parents, ['1', '3', '7'])
self.assertEqual(results['19'].children, [])
self.assertEqual(results['23'].rank, 'species')
self.assertEqual(set(results['1'].children), set(['3', '2']))
def test_build_taxid_data(self):
nodes_fp = get_data_path('nodes.dmp')
names_fp = get_data_path('names.dmp')
gi_taxid_nucl_fp = get_data_path("gi_taxid_nucl.dmp")
results = taxidtool.build_taxid_data(nodes_fp,
names_fp,
gi_taxid_nucl_fp)
for taxid, record in results.items():
self.assertEqual(record.taxid, taxid)
self.assertEqual(record.sci_name, "Node%s" % taxid)
for gi in record.assoc_gis:
self.assertTrue(gi.startswith(taxid))
self.assertEqual(results['23'].parents, ['1', '3', '7'])
self.assertEqual(results['19'].children, [])
self.assertEqual(results['23'].rank, 'species')
self.assertEqual(set(results['1'].children), set(['3', '2']))
def test_build_branch(self):
taxid_data_fp = get_data_path('taxid_data.txt')
taxid_data = taxidtool.parse_taxid_data(taxid_data_fp)
inclusion_roots = ["6"]
results = taxidtool.build_branch(taxid_data, inclusion_roots)
self.assertEqual(set(results.keys()), {'6', '16', '18', '20', '22'})
def test_build_branch(self):
taxid_data_fp = get_data_path('taxid_data.txt')
taxid_data = taxidtool.parse_taxid_data(taxid_data_fp)
inclusion_roots = ["6"]
results = taxidtool.build_branch(taxid_data, inclusion_roots)
self.assertEqual(set(results.keys()), {'6', '16', '18', '20', '22'})
def test_build_gis_to_taxids(self):
taxid_data_fp = get_data_path('taxid_data.txt')
taxid_data = taxidtool.parse_taxid_data(taxid_data_fp)
reverse_lookup = taxidtool.build_gis_to_taxids(taxid_data)
for taxid, record in taxid_data.items():
for gi in record.assoc_gis:
self.assertEqual(taxid, reverse_lookup[gi])
def test_build_gis_to_taxids(self):
taxid_data_fp = get_data_path('taxid_data.txt')
taxid_data = taxidtool.parse_taxid_data(taxid_data_fp)
reverse_lookup = taxidtool.build_gis_to_taxids(taxid_data)
for taxid, record in taxid_data.items():
for gi in record.assoc_gis:
self.assertEqual(taxid, reverse_lookup[gi])
def test_parse_nodes_dmp(self):
fp = get_data_path('nodes.dmp')
results = taxidtool.parse_nodes_dmp(fp)
for taxid, record in results.items():
self.assertEqual(record.taxid, taxid)
self.assertEqual(results['12'].parent_taxid, '4')
self.assertEqual(results['2'].rank, 'kingdom')
self.assertEqual(results['5'].parent_taxid, '3')
self.assertEqual(results['8'].rank, 'species')
def test_parse_nodes_dmp(self):
fp = get_data_path('nodes.dmp')
results = taxidtool.parse_nodes_dmp(fp)
for taxid, record in results.items():
self.assertEqual(record.taxid, taxid)
self.assertEqual(results['12'].parent_taxid, '4')
self.assertEqual(results['2'].rank, 'kingdom')
self.assertEqual(results['5'].parent_taxid, '3')
self.assertEqual(results['8'].rank, 'species')
def test_prepare(self):
indiana = Indiana(self.yax_dir, pipeline=self.arch_config_fp)
with tempfile.NamedTemporaryFile(mode='w', dir=self.yax_dir,
suffix='.ini') as fh:
config = configparser.ConfigParser()
config.read(get_data_path('test_run.ini'))
config['module3']['input_file'] = self.arch_config_fp
config['module4']['input_dir'] = self.yax_dir
config.write(fh)
fh.flush()
indiana.prepare(fh.name[:-4])
def test_prepare(self):
indiana = Indiana(self.yax_dir, pipeline=self.arch_config_fp)
with tempfile.NamedTemporaryFile(mode='w',
dir=self.yax_dir,
suffix='.ini') as fh:
config = configparser.ConfigParser()
config.read(get_data_path('test_run.ini'))
config['module3']['input_file'] = self.arch_config_fp
config['module4']['input_dir'] = self.yax_dir
config.write(fh)
fh.flush()
indiana.prepare(fh.name[:-4])
def test_parse_taxid_data(self):
taxid_data_fp = get_data_path('taxid_data.txt')
results = taxidtool.parse_taxid_data(taxid_data_fp)
for taxid, record in results.items():
self.assertEqual(record.taxid, taxid)
self.assertEqual(record.sci_name, "Node%s" % taxid)
for gi in record.assoc_gis:
self.assertTrue(gi.startswith(taxid))
self.assertEqual(results['23'].parents, ['1', '3', '7'])
self.assertEqual(results['19'].children, [])
self.assertEqual(results['23'].rank, 'species')
self.assertEqual(set(results['1'].children), set(['3', '2']))
def test_parse_taxid_data(self):
taxid_data_fp = get_data_path('taxid_data.txt')
results = taxidtool.parse_taxid_data(taxid_data_fp)
for taxid, record in results.items():
self.assertEqual(record.taxid, taxid)
self.assertEqual(record.sci_name, "Node%s" % taxid)
for gi in record.assoc_gis:
self.assertTrue(gi.startswith(taxid))
self.assertEqual(results['23'].parents, ['1', '3', '7'])
self.assertEqual(results['19'].children, [])
self.assertEqual(results['23'].rank, 'species')
self.assertEqual(set(results['1'].children), set(['3', '2']))
def setUp(self):
self._yax_dir = tempfile.TemporaryDirectory()
self.yax_dir = self._yax_dir.name
self.arch_config_fp = get_data_path('arch_config.py',
subfolder='test_pipeline')
def test_parse_names_dmp(self):
fp = get_data_path('names.dmp')
results = taxidtool.parse_names_dmp(fp)
for key, value in results.items():
self.assertEqual(value, "Node%s" % key)
def setUp(self):
self._yax_dir = tempfile.TemporaryDirectory()
self.yax_dir = self._yax_dir.name
self.arch_config_fp = get_data_path('arch_config.py',
subfolder='test_pipeline')
def test_parse_names_dmp(self):
fp = get_data_path('names.dmp')
results = taxidtool.parse_names_dmp(fp)
for key, value in results.items():
self.assertEqual(value, "Node%s" % key)
def test_parse_gi_taxid_dmp(self):
fp = get_data_path('gi_taxid_nucl.dmp')
results = taxidtool.parse_gi_taxid_dmp(fp)
for taxid, gis in results.items():
for gi in gis:
self.assertTrue(gi.startswith(taxid))
def test_parse_gi_taxid_dmp(self):
fp = get_data_path('gi_taxid_nucl.dmp')
results = taxidtool.parse_gi_taxid_dmp(fp)
for taxid, gis in results.items():
for gi in gis:
self.assertTrue(gi.startswith(taxid))