def test_premade_alignment(self):
compare_to_lanl = True
input_fn = self.fn
reference = self.reference
id = os.path.basename(input_fn)
status_file = input_fn+'_status'
#Ensure that you cannot compare to lanl if skipping alignment
with self.assertRaises(Exception):
results = hivtrace.hivtrace(id, input_fn, reference, self.ambiguities,
self.distance_threshold, self.min_overlap,
compare_to_lanl, '0.015', handle_contaminants='remove', filter_edges='remove', skip_alignment=True)
#Ensure that unequal sequence lengths fail
with self.assertRaises(Exception):
results = hivtrace.hivtrace(id, input_fn, reference, self.ambiguities,
self.distance_threshold, self.min_overlap,
False, '0.015', handle_contaminants='remove', filter_edges='remove', skip_alignment=True)
results = hivtrace.hivtrace(id, self.aligned_fn, reference, self.ambiguities,
self.distance_threshold, self.min_overlap,
False, '0.015', handle_contaminants='remove', filter_edges='remove', skip_alignment=True)
self.assertTrue('trace_results' in results.keys())
def test_premade_alignment(self):
compare_to_lanl = True
input_fn = self.fn
reference = self.reference
id = os.path.basename(input_fn)
status_file = input_fn+'_status'
#Ensure that you cannot compare to lanl if skipping alignment
with self.assertRaises(Exception):
results = hivtrace.hivtrace(id, input_fn, reference, self.ambiguities,
self.distance_threshold, self.min_overlap,
compare_to_lanl, '0.015', handle_contaminants='remove', filter_edges='remove', skip_alignment=True)
#Ensure that unequal sequence lengths fail
with self.assertRaises(Exception):
results = hivtrace.hivtrace(id, input_fn, reference, self.ambiguities,
self.distance_threshold, self.min_overlap,
False, '0.015', handle_contaminants='remove', filter_edges='remove', skip_alignment=True)
results = hivtrace.hivtrace(id, self.aligned_fn, reference, self.ambiguities,
self.distance_threshold, self.min_overlap,
False, '0.015', handle_contaminants='remove', filter_edges='remove', skip_alignment=True)
self.assertTrue('trace_results' in results.keys())
def test_env(self):
id = os.path.basename(self.env_fn)
reference = 'HXB2_env'
# run the whole thing and make sure it completed via the status file
hivtrace.hivtrace(id, self.env_fn, reference, self.ambiguities,
self.distance_threshold, self.min_overlap, False,
'0.015')
self.assertTrue(True)
def test_env(self):
compare_to_lanl = True
id = os.path.basename(self.env_fn)
reference = 'HXB2_env'
strip_drams = False
#run the whole thing and make sure it completed via the status file
hivtrace.hivtrace(id, self.env_fn, reference, self.ambiguities,
self.distance_threshold, self.min_overlap,
False, '0.015')
self.assertTrue(True)
def test_contaminant_screening_separately(self):
this_dirname = os.path.join(os.path.dirname(
os.path.realpath(__file__)))
compare_to_lanl = False
input_fn = path.join(this_dirname, 'rsrc/CONTAM.fasta')
reference = path.join(this_dirname, 'rsrc/HXB2_1497.fasta')
id = os.path.basename(input_fn)
status_file = input_fn + '_status'
results = hivtrace.hivtrace(id,
input_fn,
reference,
self.ambiguities,
self.distance_threshold,
self.min_overlap,
False,
'0.015',
handle_contaminants='separately',
filter_edges='remove',
skip_alignment=True)
self.assertTrue("contaminant_sequences" in results["trace_results"]
["Network Summary"])
def test_contaminant_annotations(self):
this_dirname = os.path.join(os.path.dirname(
os.path.realpath(__file__)))
compare_to_lanl = False
input_fn = path.join(this_dirname, 'rsrc/CONTAM.fasta')
reference = self.reference
id = os.path.basename(input_fn)
status_file = input_fn + '_status'
results = hivtrace.hivtrace(id,
input_fn,
reference,
self.ambiguities,
self.distance_threshold,
self.min_overlap,
False,
'0.015',
handle_contaminants='report',
filter_edges='remove',
skip_alignment=True)
nodes = list(
filter(lambda x: "HXB2" in x["id"],
results["trace_results"]["Nodes"]))
self.assertTrue(all('problematic' in n["attributes"] for n in nodes))
def test_keep_singletons(self):
this_dirname = os.path.join(os.path.dirname(
os.path.realpath(__file__)))
compare_to_lanl = False
#input_fn = self.fn
input_fn = path.join(this_dirname, 'rsrc/TEST2.FASTA')
reference = self.reference
id = os.path.basename(input_fn)
status_file = input_fn + '_status'
results = hivtrace.hivtrace(id,
input_fn,
reference,
self.ambiguities,
self.distance_threshold,
self.min_overlap,
False,
'0.015',
handle_contaminants='report',
filter_edges='remove',
skip_alignment=True)
self.assertTrue('Singletons' in results['trace_results'].keys())
def test_strip_reference_sequences(self):
id = os.path.basename(self.fn)
compare_to_lanl = False
##run the whole thing and make sure it completed via the status file
results = hivtrace.hivtrace(id, self.fn, self.reference,
self.ambiguities, self.distance_threshold,
self.min_overlap, compare_to_lanl, '0.025')
[
self.assertTrue("removed" in edge)
for edge in results["trace_results"]["Edges"]
]
# Read output json
known_contaminants = [
'B|FR|A04321|1983', '08_BC_HXB2_SABOTAGE|CN|AB078686|2000'
]
[
self.assertTrue(not any([k in node for k in known_contaminants]))
for node in results["trace_results"]["Nodes"]
]
return
def test_empty_contaminants(self):
compare_to_lanl = False
input_fn = self.fn
reference = self.reference
id = os.path.basename(input_fn)
status_file = input_fn+'_status'
#run the whole thing and make sure it completed via the status file
results = hivtrace.hivtrace(id, input_fn, reference, self.ambiguities,
self.distance_threshold, self.min_overlap,
False, '0.015', handle_contaminants='remove', filter_edges='remove')
def test_empty_contaminants(self):
compare_to_lanl = False
input_fn = self.fn
reference = self.reference
id = os.path.basename(input_fn)
status_file = input_fn+'_status'
#run the whole thing and make sure it completed via the status file
results = hivtrace.hivtrace(id, input_fn, reference, self.ambiguities,
self.distance_threshold, self.min_overlap,
False, '0.015', handle_contaminants='remove', filter_edges='remove')
def test_keep_singletons(self):
this_dirname = os.path.join(os.path.dirname(os.path.realpath(__file__)))
compare_to_lanl = False
#input_fn = self.fn
input_fn = path.join(this_dirname, 'rsrc/TEST2.FASTA')
reference = self.reference
id = os.path.basename(input_fn)
status_file = input_fn+'_status'
results = hivtrace.hivtrace(id, input_fn, reference, self.ambiguities,
self.distance_threshold, self.min_overlap,
False, '0.015', handle_contaminants='report', filter_edges='remove', skip_alignment=True)
self.assertTrue('Singletons' in results['trace_results'].keys())
def test_contaminant_annotations(self):
this_dirname = os.path.join(os.path.dirname(os.path.realpath(__file__)))
compare_to_lanl = False
#input_fn = self.fn
input_fn = path.join(this_dirname, 'rsrc/CONTAM.fasta')
reference = self.reference
id = os.path.basename(input_fn)
status_file = input_fn+'_status'
results = hivtrace.hivtrace(id, input_fn, reference, self.ambiguities,
self.distance_threshold, self.min_overlap,
False, '0.015', handle_contaminants='report', filter_edges='remove', skip_alignment=True)
nodes = list(filter(lambda x: "HXB2" in x["id"], results["trace_results"]["Nodes"]))
self.assertTrue(all('problematic' in n["attributes"] for n in nodes))
def test_hivtrace_lanl(self):
id = os.path.basename(self.fn)
compare_to_lanl = True
#run the whole thing and make sure it completed via the status file
results = hivtrace.hivtrace(id, self.fn, self.reference, self.ambiguities,
self.distance_threshold, self.min_overlap,
compare_to_lanl, '0.025', False, "report")
# Read output json
self.assertTrue(results["lanl_trace_results"]["Network Summary"]["Clusters"] == 2)
self.assertTrue(results["lanl_trace_results"]["Network Summary"]["Edges"] == 31)
self.assertTrue(results["lanl_trace_results"]["Network Summary"]["Nodes"] == 13)
self.assertTrue(set(results["lanl_trace_results"].keys()) == set(['Cluster sizes', 'Edge Stages', 'Edges', 'HIV Stages', 'Network Summary', 'Settings', 'Degrees', 'Directed Edges', 'Multiple sequences', 'Nodes']))
return
def test_strip_reference_sequences(self):
id = os.path.basename(self.fn)
compare_to_lanl = False
##run the whole thing and make sure it completed via the status file
results = hivtrace.hivtrace(id, self.fn, self.reference, self.ambiguities,
self.distance_threshold, self.min_overlap,
compare_to_lanl, '0.025')
[self.assertTrue("removed" in edge) for edge in results["trace_results"]["Edges"]]
# Read output json
known_contaminants = ['B|FR|A04321|1983', '08_BC_HXB2_SABOTAGE|CN|AB078686|2000']
[self.assertTrue(not any([k in node for k in known_contaminants])) for node in results["trace_results"]["Nodes"]]
return
def test_strip_drams(self):
#run the whole thing and make sure it completed via the status file
results = strip_drams(self.fn, 'lewis')
self.assertTrue(results.__next__()[1][120:123] == '---')
self.assertTrue(results.__next__()[1][672:675] == '---')
self.assertFalse(results.__next__()[1][687:690] == '---')
results = strip_drams(self.fn, 'wheeler')
self.assertTrue(results.__next__()[1][129:132] == '---')
self.assertTrue(results.__next__()[1][687:690] == '---')
results = hivtrace.hivtrace(id, self.fn, self.reference,
self.ambiguities, self.distance_threshold,
self.min_overlap, False, '0.025', 'lewis')
self.assertTrue(results["trace_results"])
return
def test_custom_reference(self):
compare_to_lanl = True
input_fn = self.fn
reference = self.custom_reference
id = os.path.basename(input_fn)
status_file = input_fn+'_status'
known_contaminants = ['Z|JP|K03455|2036|7']
#run the whole thing and make sure it completed via the status file
results = hivtrace.hivtrace(id, input_fn, reference, self.ambiguities,
self.distance_threshold, self.min_overlap,
False, '0.015')
# Read output json
known_contaminants = ['B|FR|A04321|1983', '08_BC_HXB2_SABOTAGE|CN|AB078686|2000']
[self.assertTrue(not any([k in node for k in known_contaminants])) for node in results["trace_results"]["Nodes"]]
def test_custom_reference(self):
compare_to_lanl = True
input_fn = self.fn
reference = self.custom_reference
id = os.path.basename(input_fn)
status_file = input_fn+'_status'
known_contaminants = ['Z|JP|K03455|2036|7']
#run the whole thing and make sure it completed via the status file
results = hivtrace.hivtrace(id, input_fn, reference, self.ambiguities,
self.distance_threshold, self.min_overlap,
False, '0.015')
# Read output json
known_contaminants = ['B|FR|A04321|1983', '08_BC_HXB2_SABOTAGE|CN|AB078686|2000']
[self.assertTrue(not any([k in node for k in known_contaminants])) for node in results["trace_results"]["Nodes"]]
def test_strip_drams(self):
#run the whole thing and make sure it completed via the status file
results = strip_drams(self.fn, 'lewis')
self.assertTrue(results.__next__()[1][120:123] == '---')
self.assertTrue(results.__next__()[1][672:675] == '---')
self.assertFalse(results.__next__()[1][687:690] == '---')
results = strip_drams(self.fn, 'wheeler')
self.assertTrue(results.__next__()[1][129:132] == '---')
self.assertTrue(results.__next__()[1][687:690] == '---')
results = hivtrace.hivtrace(id, self.fn, self.reference, self.ambiguities,
self.distance_threshold, self.min_overlap,
False, '0.025', 'lewis')
self.assertTrue(results["trace_results"])
return
