def test_integrase_position(self):
xml = """\
<ALGORITHM>
<ALGNAME>HIVDB</ALGNAME>
<ALGVERSION>fake</ALGVERSION>
<ALGDATE>2017-03-02</ALGDATE>
<DEFINITIONS>
<GENE_DEFINITION>
<NAME>IN</NAME>
<DRUGCLASSLIST>INSTI</DRUGCLASSLIST>
</GENE_DEFINITION>
<LEVEL_DEFINITION>
<ORDER>1</ORDER>
<ORIGINAL>Susceptible</ORIGINAL>
<SIR>S</SIR>
</LEVEL_DEFINITION>
<LEVEL_DEFINITION>
<ORDER>5</ORDER>
<ORIGINAL>High-Level Resistance</ORIGINAL>
<SIR>R</SIR>
</LEVEL_DEFINITION>
<DRUGCLASS>
<NAME>INSTI</NAME>
<DRUGLIST>BIC</DRUGLIST>
</DRUGCLASS>
<GLOBALRANGE><![CDATA[(-INF TO 9 => 1, 10 TO INF => 5)]]></GLOBALRANGE>
<COMMENT_DEFINITIONS>
</COMMENT_DEFINITIONS>
</DEFINITIONS>
<DRUG>
<NAME>BIC</NAME>
<FULLNAME>bictegravir</FULLNAME>
<RULE>
<CONDITION><![CDATA[SCORE FROM(51Y => 10)]]></CONDITION>
<ACTIONS>
<SCORERANGE>
<USE_GLOBALRANGE/>
</SCORERANGE>
</ACTIONS>
</RULE>
</DRUG>
<MUTATION_COMMENTS>
</MUTATION_COMMENTS>
</ALGORITHM>
"""
asi = AsiAlgorithm(StringIO(xml))
expected_positions = {51}
positions = asi.get_gene_positions('INT')
self.assertEqual(expected_positions, positions)
def test_integrase_position(self):
xml = """\
<ALGORITHM>
<ALGNAME>HIVDB</ALGNAME>
<ALGVERSION>fake</ALGVERSION>
<ALGDATE>2017-03-02</ALGDATE>
<DEFINITIONS>
<GENE_DEFINITION>
<NAME>IN</NAME>
<DRUGCLASSLIST>INSTI</DRUGCLASSLIST>
</GENE_DEFINITION>
<LEVEL_DEFINITION>
<ORDER>1</ORDER>
<ORIGINAL>Susceptible</ORIGINAL>
<SIR>S</SIR>
</LEVEL_DEFINITION>
<LEVEL_DEFINITION>
<ORDER>5</ORDER>
<ORIGINAL>High-Level Resistance</ORIGINAL>
<SIR>R</SIR>
</LEVEL_DEFINITION>
<DRUGCLASS>
<NAME>INSTI</NAME>
<DRUGLIST>BIC</DRUGLIST>
</DRUGCLASS>
<GLOBALRANGE><![CDATA[(-INF TO 9 => 1, 10 TO INF => 5)]]></GLOBALRANGE>
<COMMENT_DEFINITIONS>
</COMMENT_DEFINITIONS>
</DEFINITIONS>
<DRUG>
<NAME>BIC</NAME>
<FULLNAME>bictegravir</FULLNAME>
<RULE>
<CONDITION><![CDATA[SCORE FROM(51Y => 10)]]></CONDITION>
<ACTIONS>
<SCORERANGE>
<USE_GLOBALRANGE/>
</SCORERANGE>
</ACTIONS>
</RULE>
</DRUG>
<MUTATION_COMMENTS>
</MUTATION_COMMENTS>
</ALGORITHM>
"""
asi = AsiAlgorithm(StringIO(xml))
expected_positions = {51}
positions = asi.get_gene_positions('INT')
self.assertEqual(expected_positions, positions)
def test_not_available(self):
asi = AsiAlgorithm(rules_yaml=self.default_drugs,
genotype='3',
references=self.references)
aa_seq = [['A']] * 100
compared_attrs = ('code', 'score', 'level', 'level_name')
expected_drugs = [('MDP', 0.0, -1, 'Resistance Interpretation Not Available'),
('SIL', 0.0, 2, 'Not Indicated')]
expected_mutation_comments = []
result = asi.interpret(aa_seq, 'HCV3-S52-NS5a')
drugs = list(map(attrgetter(*compared_attrs), result.drugs))
self.assertEqual(expected_drugs, drugs)
self.assertEqual(expected_mutation_comments, result.mutation_comments)
def test_not_available(self):
asi = AsiAlgorithm(rules_yaml=self.default_drugs,
genotype='3',
references=self.references)
aa_seq = [['A']] * 100
compared_attrs = ('code', 'score', 'level', 'level_name')
expected_drugs = [('MDP', 0.0, -1, 'Resistance Interpretation Not Available'),
('SIL', 0.0, 2, 'Not Indicated')]
expected_mutation_comments = []
result = asi.interpret(aa_seq, 'HCV3-S52-NS5a')
drugs = list(map(attrgetter(*compared_attrs), result.drugs))
self.assertEqual(expected_drugs, drugs)
self.assertEqual(expected_mutation_comments, result.mutation_comments)
def test_flag_only(self):
asi = AsiAlgorithm(rules_yaml=self.default_drugs,
genotype='1B',
references=self.references)
aa_seq = [['A']] * 42 + [['L']] + [['A']] * 57
compared_attrs = ('code', 'score', 'level', 'level_name')
expected_drugs = [('MDP', 0.0, 3, 'Mutations Detected; Effect Unknown'),
('SIL', 0.0, 3, 'Mutations Detected; Effect Unknown')]
expected_mutation_comments = []
result = asi.interpret(aa_seq, 'HCV1B-Con1-NS5a')
drugs = list(map(attrgetter(*compared_attrs), result.drugs))
self.assertEqual(expected_drugs, drugs)
self.assertEqual(expected_mutation_comments, result.mutation_comments)
def test_score_and_flag(self):
asi = AsiAlgorithm(rules_yaml=self.default_drugs,
genotype='1B',
references=self.references)
aa_seq = [['A']] * 41 + [['L']] * 2 + [['A']] * 57
compared_attrs = ('code', 'score', 'level', 'level_name')
expected_drugs = [('MDP', 8.0, 5, 'Resistance Likely'),
('SIL', 8.0, 5, 'Resistance Likely')]
expected_mutation_comments = []
result = asi.interpret(aa_seq, 'HCV1B-Con1-NS5a')
drugs = list(map(attrgetter(*compared_attrs), result.drugs))
self.assertEqual(expected_drugs, drugs)
self.assertEqual(expected_mutation_comments, result.mutation_comments)
def test_interpret(self):
asi = AsiAlgorithm(rules_yaml=self.default_drugs,
genotype='1A',
references=self.references)
aa_seq = [['A']] * 40 + [['L']] + [['A']] * 59
compared_attrs = ('code', 'score', 'level', 'level_name')
expected_drugs = [('MDP', 4.0, 4, 'Resistance Possible'),
('SIL', 4.0, 4, 'Resistance Possible')]
expected_mutation_comments = []
result = asi.interpret(aa_seq, 'HCV1A-H77-NS5a')
drugs = list(map(attrgetter(*compared_attrs), result.drugs))
self.assertEqual(expected_drugs, drugs)
self.assertEqual(expected_mutation_comments, result.mutation_comments)
def test_interpret(self):
asi = AsiAlgorithm(rules_yaml=self.default_drugs,
genotype='1A',
references=self.references)
aa_seq = [['A']] * 40 + [['L']] + [['A']] * 59
compared_attrs = ('code', 'score', 'level', 'level_name')
expected_drugs = [('MDP', 4.0, 4, 'Resistance Possible'),
('SIL', 4.0, 4, 'Resistance Possible')]
expected_mutation_comments = []
result = asi.interpret(aa_seq, 'HCV1A-H77-NS5a')
drugs = list(map(attrgetter(*compared_attrs), result.drugs))
self.assertEqual(expected_drugs, drugs)
self.assertEqual(expected_mutation_comments, result.mutation_comments)
def test_score_and_flag(self):
asi = AsiAlgorithm(rules_yaml=self.default_drugs,
genotype='1B',
references=self.references)
aa_seq = [['A']] * 41 + [['L']] * 2 + [['A']] * 57
compared_attrs = ('code', 'score', 'level', 'level_name')
expected_drugs = [('MDP', 8.0, 5, 'Resistance Likely'),
('SIL', 8.0, 5, 'Resistance Likely')]
expected_mutation_comments = []
result = asi.interpret(aa_seq, 'HCV1B-Con1-NS5a')
drugs = list(map(attrgetter(*compared_attrs), result.drugs))
self.assertEqual(expected_drugs, drugs)
self.assertEqual(expected_mutation_comments, result.mutation_comments)
def test_flag_only(self):
asi = AsiAlgorithm(rules_yaml=self.default_drugs,
genotype='1B',
references=self.references)
aa_seq = [['A']] * 42 + [['L']] + [['A']] * 57
compared_attrs = ('code', 'score', 'level', 'level_name')
expected_drugs = [('MDP', 0.0, 3, 'Mutations Detected; Effect Unknown'),
('SIL', 0.0, 3, 'Mutations Detected; Effect Unknown')]
expected_mutation_comments = []
result = asi.interpret(aa_seq, 'HCV1B-Con1-NS5a')
drugs = list(map(attrgetter(*compared_attrs), result.drugs))
self.assertEqual(expected_drugs, drugs)
self.assertEqual(expected_mutation_comments, result.mutation_comments)
def load_asi():
asi = AsiAlgorithm(HIV_RULES_PATH)
algorithms = {None: asi}
with open(HCV_RULES_PATH) as f:
hcv_rules = yaml.safe_load(f)
genotypes = {genotype['genotype']
for rule in hcv_rules
for genotype in rule['genotypes']}
for genotype in genotypes:
if len(genotype) > 1 and genotype[0] in genotypes:
backup_genotype = genotype[0]
else:
backup_genotype = None
asi = AsiAlgorithm(rules_yaml=hcv_rules,
genotype=genotype,
backup_genotype=backup_genotype)
algorithms[genotype] = asi
return algorithms
def test_low_coverage(self):
asi = AsiAlgorithm(rules_yaml=self.default_drugs,
genotype='1A',
references=self.references)
aa_seq = [[]] * 100
compared_attrs = ('code', 'score', 'level', 'level_name')
expected_drugs = [('MDP',
0.0,
0,
'Sequence does not meet quality-control standards'),
('SIL',
0.0,
0,
'Sequence does not meet quality-control standards')]
expected_mutation_comments = []
result = asi.interpret(aa_seq, 'HCV1A-H77-NS5a')
drugs = list(map(attrgetter(*compared_attrs), result.drugs))
self.assertEqual(expected_drugs, drugs)
self.assertEqual(expected_mutation_comments, result.mutation_comments)
def test_low_coverage(self):
asi = AsiAlgorithm(rules_yaml=self.default_drugs,
genotype='1A',
references=self.references)
aa_seq = [[]] * 100
compared_attrs = ('code', 'score', 'level', 'level_name')
expected_drugs = [('MDP',
0.0,
0,
'Sequence does not meet quality-control standards'),
('SIL',
0.0,
0,
'Sequence does not meet quality-control standards')]
expected_mutation_comments = []
result = asi.interpret(aa_seq, 'HCV1A-H77-NS5a')
drugs = list(map(attrgetter(*compared_attrs), result.drugs))
self.assertEqual(expected_drugs, drugs)
self.assertEqual(expected_mutation_comments, result.mutation_comments)
def create_asi(drugs=default_drugs, comments=default_comments):
xml = """\
<ALGORITHM>
<ALGNAME>HIVDB</ALGNAME>
<ALGVERSION>fake</ALGVERSION>
<ALGDATE>2017-03-02</ALGDATE>
<DEFINITIONS>
<GENE_DEFINITION>
<NAME>RT</NAME>
<DRUGCLASSLIST>NRTI</DRUGCLASSLIST>
</GENE_DEFINITION>
<LEVEL_DEFINITION>
<ORDER>1</ORDER>
<ORIGINAL>Susceptible</ORIGINAL>
<SIR>S</SIR>
</LEVEL_DEFINITION>
<LEVEL_DEFINITION>
<ORDER>5</ORDER>
<ORIGINAL>High-Level Resistance</ORIGINAL>
<SIR>R</SIR>
</LEVEL_DEFINITION>
<DRUGCLASS>
<NAME>NRTI</NAME>
<DRUGLIST>ABC</DRUGLIST>
</DRUGCLASS>
<GLOBALRANGE><![CDATA[(-INF TO 9 => 1, 10 TO INF => 5)]]></GLOBALRANGE>
<COMMENT_DEFINITIONS>
{comments}
</COMMENT_DEFINITIONS>
</DEFINITIONS>
{drugs}
<MUTATION_COMMENTS>
</MUTATION_COMMENTS>
</ALGORITHM>
""".format(drugs=drugs, comments=comments)
return AsiAlgorithm(StringIO(xml))
class AsiAlgorithmTest(TestCase):
def setUp(self):
self.asi = AsiAlgorithm(os.path.join(os.path.dirname(__file__),
"..",
"resistance",
"HIVDB_8.8.xml"))
def test_interpret(self):
aa_seq = [[amino] for amino in self.asi.stds['RT']]
aa_seq[40] = ['L'] # Resistance mutation.
compared_attrs = ('code', 'score', 'level', 'level_name')
expected_drugs = [('3TC', 0.0, 1, 'Susceptible'),
('ABC', 5.0, 1, 'Susceptible'),
('AZT', 15.0, 3, 'Low-Level Resistance'),
('D4T', 15.0, 3, 'Low-Level Resistance'),
('DDI', 10.0, 2, 'Susceptible'),
('FTC', 0.0, 1, 'Susceptible'),
('TDF', 5.0, 1, 'Susceptible'),
('DOR', 0.0, 1, 'Susceptible'),
('EFV', 0.0, 1, 'Susceptible'),
('ETR', 0.0, 1, 'Susceptible'),
('NVP', 0.0, 1, 'Susceptible'),
('RPV', 0.0, 1, 'Susceptible')]
# The L234I message looks like a bug in the HIVdb rules.
# We don't actually use the comments, so ignore the problem for now.
expected_mutation_comments = [
'L234I is a nonpolymorphic mutation selected in persons receiving NVP and '
'EFV. It is also selected in vitro by ETR and DOR. In combination with V106A, '
'it is associated with high-level DOR resistance. Its effect on '
'susceptibility when it occurs alone has not been studied. V108V is a highly '
'unusual mutation at this position.',
'M41L is a TAM that usually occurs with T215Y. In combination, '
'M41L plus T215Y confer intermediate / high-level resistance to '
'AZT and d4T and contribute to reduced ddI, ABC and TDF '
'susceptibility.']
result = self.asi.interpret(aa_seq, 'RT')
drugs = list(map(attrgetter(*compared_attrs), result.drugs))
assert expected_drugs == drugs
assert expected_mutation_comments == result.mutation_comments
def test_protease(self):
aa_seq = [[amino] for amino in self.asi.stds['PR']]
aa_seq[23] = ['I'] # Resistance mutation.
compared_attrs = ('code', 'score', 'level', 'level_name')
expected_drugs = [('ATV/r', 10.0, 2, 'Susceptible'),
('DRV/r', 0.0, 1, 'Susceptible'),
('FPV/r', 10.0, 2, 'Susceptible'),
('IDV/r', 15.0, 3, 'Low-Level Resistance'),
('LPV/r', 10.0, 2, 'Susceptible'),
('NFV', 10.0, 2, 'Susceptible'),
('SQV/r', 10.0, 2, 'Susceptible'),
('TPV/r', -5.0, 1, 'Susceptible')]
expected_mutation_comments = [
'L24I is a non-polymorphic mutation selected by IDV and LPV. It '
'contributes reduced susceptibility to each PI except DRV and TPV.']
result = self.asi.interpret(aa_seq, 'PR')
drugs = list(map(attrgetter(*compared_attrs), result.drugs))
self.assertEqual(expected_drugs, drugs)
self.assertEqual(expected_mutation_comments, result.mutation_comments)
def test_integrase(self):
aa_seq = [[amino] for amino in self.asi.stds['IN']]
aa_seq[50] = ['Y'] # Resistance mutation.
compared_attrs = ('code', 'score', 'level', 'level_name')
expected_drugs = [('BIC', 10.0, 2, 'Susceptible'),
('DTG', 10.0, 2, 'Susceptible'),
('EVG', 15.0, 3, 'Low-Level Resistance'),
('RAL', 15.0, 3, 'Low-Level Resistance')]
expected_mutation_comments = [
'H51Y is a rare non-polymorphic accessory mutation selected in '
'patients receiving RAL and EVG and in vitro by DTG. H51Y '
'minimally reduces EVG susceptibility (~2 to 3-fold). It does not '
'reduce RAL or DTG susceptibility.']
result = self.asi.interpret(aa_seq, 'IN')
drugs = list(map(attrgetter(*compared_attrs), result.drugs))
assert expected_drugs == drugs
assert expected_mutation_comments == result.mutation_comments
def test_integrase_no_coverage(self):
aa_seq = [[]] * len(self.asi.stds['IN'])
compared_attrs = ('code', 'score', 'level', 'level_name')
expected_drugs = [('BIC', 0.0, 0, 'Sequence does not meet quality-control standards'),
('DTG', 0.0, 0, 'Sequence does not meet quality-control standards'),
('EVG', 0.0, 0, 'Sequence does not meet quality-control standards'),
('RAL', 0.0, 0, 'Sequence does not meet quality-control standards')]
expected_mutation_comments = []
result = self.asi.interpret(aa_seq, 'IN')
drugs = list(map(attrgetter(*compared_attrs), result.drugs))
assert expected_drugs == drugs
assert expected_mutation_comments == result.mutation_comments
def test_comment_filter(self):
aa_seq = [[amino] for amino in self.asi.stds['PR']]
aa_seq[23] = ['D']
expected_mutation_comments = [
'L24I is a non-polymorphic mutation selected by IDV and LPV. It '
'contributes reduced susceptibility to each PI except DRV and TPV. '
'L24D is a highly unusual mutation at this position.']
result = self.asi.interpret(aa_seq, 'PR')
self.assertEqual(expected_mutation_comments, result.mutation_comments)
def test_gaps(self):
aa_seq = [{c: 1.0} for c in self.asi.stds['PR']]
aa_seq[23] = {'I': 1.0}
compared_attrs = ('code', 'score', 'level', 'level_name')
expected_drugs = [('ATV/r', 10.0, 2, 'Susceptible'),
('DRV/r', 0.0, 1, 'Susceptible'),
('FPV/r', 10.0, 2, 'Susceptible'),
('IDV/r', 15.0, 3, 'Low-Level Resistance'),
('LPV/r', 10.0, 2, 'Susceptible'),
('NFV', 10.0, 2, 'Susceptible'),
('SQV/r', 10.0, 2, 'Susceptible'),
('TPV/r', -5.0, 1, 'Susceptible')]
expected_mutation_comments = [
'L24I is a non-polymorphic mutation selected by IDV and LPV. It '
'contributes reduced susceptibility to each PI except DRV and TPV.']
result = self.asi.interpret(aa_seq, 'PR')
drugs = list(map(attrgetter(*compared_attrs), result.drugs))
self.assertEqual(expected_drugs, drugs)
self.assertEqual(expected_mutation_comments, result.mutation_comments)
def test_multiple_regions(self):
aa_seq1 = [{c: 1.0} for c in self.asi.stds['RT']]
aa_seq1[40] = {'L': 1.0}
aa_seq2 = [{c: 1.0} for c in self.asi.stds['PR']]
aa_seq2[23] = {'I': 1.0}
compared_attrs = ('code', 'score', 'level', 'level_name')
expected_drugs = [('ATV/r', 10.0, 2, 'Susceptible'),
('DRV/r', 0.0, 1, 'Susceptible'),
('FPV/r', 10.0, 2, 'Susceptible'),
('IDV/r', 15.0, 3, 'Low-Level Resistance'),
('LPV/r', 10.0, 2, 'Susceptible'),
('NFV', 10.0, 2, 'Susceptible'),
('SQV/r', 10.0, 2, 'Susceptible'),
('TPV/r', -5.0, 1, 'Susceptible')]
expected_mutation_comments = [
'L24I is a non-polymorphic mutation selected by IDV and LPV. It '
'contributes reduced susceptibility to each PI except DRV and TPV.']
self.asi.interpret(aa_seq1, 'RT')
result = self.asi.interpret(aa_seq2, 'PR')
drugs = list(map(attrgetter(*compared_attrs), result.drugs))
self.assertEqual(expected_drugs, drugs)
self.assertEqual(expected_mutation_comments, result.mutation_comments)
def test_mutations(self):
aa_seq = [[amino] for amino in self.asi.stds['RT']]
self.assertEqual(['E'], aa_seq[39])
aa_seq[39] = ['L']
self.assertEqual(['M'], aa_seq[40])
aa_seq[40] = ['L']
expected_mutations = {'NRTI': ['M41L'], 'NNRTI': []}
result = self.asi.interpret(aa_seq, 'RT')
self.assertEqual(expected_mutations, result.mutations)
def test_mutations_have_wildtype(self):
aa_seq = [[amino] for amino in self.asi.stds['RT']]
self.assertEqual(['M'], aa_seq[40])
aa_seq[40] = ['L', 'R']
expected_mutations = {'NRTI': ['M41L'], 'NNRTI': []}
result = self.asi.interpret(aa_seq, 'RT')
self.assertEqual(expected_mutations, result.mutations)
def test_drug_classes(self):
aa_seq = [[]] * 440
compared_attrs = ('code', 'name', 'drug_class')
expected_drugs = [('3TC', 'lamivudine', 'NRTI'),
('ABC', 'abacavir', 'NRTI'),
('AZT', 'zidovudine', 'NRTI'),
('D4T', 'stavudine', 'NRTI'),
('DDI', 'didanosine', 'NRTI'),
('FTC', 'emtricitabine', 'NRTI'),
('TDF', 'tenofovir', 'NRTI'),
('DOR', 'doravirine', 'NNRTI'),
('EFV', 'efavirenz', 'NNRTI'),
('ETR', 'etravirine', 'NNRTI'),
('NVP', 'nevirapine', 'NNRTI'),
('RPV', 'rilpivirine', 'NNRTI')]
result = self.asi.interpret(aa_seq, 'RT')
drugs = list(map(attrgetter(*compared_attrs), result.drugs))
self.assertEqual(expected_drugs, drugs)
def setUp(self):
self.asi = AsiAlgorithm(os.path.join(os.path.dirname(__file__),
"..",
"resistance",
"HIVDB_8.3.xml"))
class AsiAlgorithmTest(TestCase):
def setUp(self):
self.asi = AsiAlgorithm(os.path.join(os.path.dirname(__file__),
"..",
"resistance",
"HIVDB_8.3.xml"))
def test_interpret(self):
aa_seq = [[amino] for amino in self.asi.stds['RT']]
aa_seq[40] = ['L']
compared_attrs = ('code', 'score', 'level', 'level_name')
expected_drugs = [('3TC', 0.0, 1, 'Susceptible'),
('ABC', 5.0, 1, 'Susceptible'),
('AZT', 15.0, 3, 'Low-Level Resistance'),
('D4T', 15.0, 3, 'Low-Level Resistance'),
('DDI', 10.0, 2, 'Susceptible'),
('FTC', 0.0, 1, 'Susceptible'),
('TDF', 5.0, 1, 'Susceptible'),
('EFV', 0.0, 1, 'Susceptible'),
('ETR', 0.0, 1, 'Susceptible'),
('NVP', 0.0, 1, 'Susceptible'),
('RPV', 0.0, 1, 'Susceptible')]
expected_mutation_comments = [
'M41L is a TAM that usually occurs with T215Y. In combination, '
'M41L plus T215Y confer intermediate / high-level resistance to '
'AZT and d4T and contribute to reduced ddI, ABC and TDF '
'susceptibility.']
result = self.asi.interpret(aa_seq, 'RT')
drugs = list(map(attrgetter(*compared_attrs), result.drugs))
self.assertEqual(expected_drugs, drugs)
self.assertEqual(expected_mutation_comments, result.mutation_comments)
def test_protease(self):
aa_seq = [[amino] for amino in self.asi.stds['PR']]
aa_seq[23] = ['I']
compared_attrs = ('code', 'score', 'level', 'level_name')
expected_drugs = [('ATV/r', 10.0, 2, 'Susceptible'),
('DRV/r', 0.0, 1, 'Susceptible'),
('FPV/r', 10.0, 2, 'Susceptible'),
('IDV/r', 15.0, 3, 'Low-Level Resistance'),
('LPV/r', 10.0, 2, 'Susceptible'),
('NFV', 10.0, 2, 'Susceptible'),
('SQV/r', 10.0, 2, 'Susceptible'),
('TPV/r', -5.0, 1, 'Susceptible')]
expected_mutation_comments = [
'L24I is a non-polymorphic mutation selected by IDV and LPV. It '
'contributes reduced susceptibility to each PI except DRV and TPV.']
result = self.asi.interpret(aa_seq, 'PR')
drugs = list(map(attrgetter(*compared_attrs), result.drugs))
self.assertEqual(expected_drugs, drugs)
self.assertEqual(expected_mutation_comments, result.mutation_comments)
def test_comment_filter(self):
aa_seq = [[amino] for amino in self.asi.stds['PR']]
aa_seq[23] = ['D']
expected_mutation_comments = [
'L24I is a non-polymorphic mutation selected by IDV and LPV. It '
'contributes reduced susceptibility to each PI except DRV and TPV. '
'L24D is a highly unusual mutation at this position.']
result = self.asi.interpret(aa_seq, 'PR')
self.assertEqual(expected_mutation_comments, result.mutation_comments)
def test_gaps(self):
aa_seq = [{c: 1.0} for c in self.asi.stds['PR']]
aa_seq[23] = {'I': 1.0}
compared_attrs = ('code', 'score', 'level', 'level_name')
expected_drugs = [('ATV/r', 10.0, 2, 'Susceptible'),
('DRV/r', 0.0, 1, 'Susceptible'),
('FPV/r', 10.0, 2, 'Susceptible'),
('IDV/r', 15.0, 3, 'Low-Level Resistance'),
('LPV/r', 10.0, 2, 'Susceptible'),
('NFV', 10.0, 2, 'Susceptible'),
('SQV/r', 10.0, 2, 'Susceptible'),
('TPV/r', -5.0, 1, 'Susceptible')]
expected_mutation_comments = [
'L24I is a non-polymorphic mutation selected by IDV and LPV. It '
'contributes reduced susceptibility to each PI except DRV and TPV.']
result = self.asi.interpret(aa_seq, 'PR')
drugs = list(map(attrgetter(*compared_attrs), result.drugs))
self.assertEqual(expected_drugs, drugs)
self.assertEqual(expected_mutation_comments, result.mutation_comments)
def test_multiple_regions(self):
aa_seq1 = [{c: 1.0} for c in self.asi.stds['RT']]
aa_seq1[40] = {'L': 1.0}
aa_seq2 = [{c: 1.0} for c in self.asi.stds['PR']]
aa_seq2[23] = {'I': 1.0}
compared_attrs = ('code', 'score', 'level', 'level_name')
expected_drugs = [('ATV/r', 10.0, 2, 'Susceptible'),
('DRV/r', 0.0, 1, 'Susceptible'),
('FPV/r', 10.0, 2, 'Susceptible'),
('IDV/r', 15.0, 3, 'Low-Level Resistance'),
('LPV/r', 10.0, 2, 'Susceptible'),
('NFV', 10.0, 2, 'Susceptible'),
('SQV/r', 10.0, 2, 'Susceptible'),
('TPV/r', -5.0, 1, 'Susceptible')]
expected_mutation_comments = [
'L24I is a non-polymorphic mutation selected by IDV and LPV. It '
'contributes reduced susceptibility to each PI except DRV and TPV.']
self.asi.interpret(aa_seq1, 'RT')
result = self.asi.interpret(aa_seq2, 'PR')
drugs = list(map(attrgetter(*compared_attrs), result.drugs))
self.assertEqual(expected_drugs, drugs)
self.assertEqual(expected_mutation_comments, result.mutation_comments)
def test_mutations(self):
aa_seq = [[amino] for amino in self.asi.stds['RT']]
self.assertEqual(['E'], aa_seq[39])
aa_seq[39] = ['L']
self.assertEqual(['M'], aa_seq[40])
aa_seq[40] = ['L']
expected_mutations = {'NRTI': ['M41L'], 'NNRTI': []}
result = self.asi.interpret(aa_seq, 'RT')
self.assertEqual(expected_mutations, result.mutations)
def test_mutations_have_wildtype(self):
aa_seq = [[amino] for amino in self.asi.stds['RT']]
self.assertEqual(['M'], aa_seq[40])
aa_seq[40] = ['L', 'R']
expected_mutations = {'NRTI': ['M41L'], 'NNRTI': []}
result = self.asi.interpret(aa_seq, 'RT')
self.assertEqual(expected_mutations, result.mutations)
def test_drug_classes(self):
aa_seq = [[]] * 440
compared_attrs = ('code', 'name', 'drug_class')
expected_drugs = [('3TC', 'lamivudine', 'NRTI'),
('ABC', 'abacavir', 'NRTI'),
('AZT', 'zidovudine', 'NRTI'),
('D4T', 'stavudine', 'NRTI'),
('DDI', 'didanosine', 'NRTI'),
('FTC', 'emtricitabine', 'NRTI'),
('TDF', 'tenofovir', 'NRTI'),
('EFV', 'efavirenz', 'NNRTI'),
('ETR', 'etravirine', 'NNRTI'),
('NVP', 'nevirapine', 'NNRTI'),
('RPV', 'rilpivirine', 'NNRTI')]
result = self.asi.interpret(aa_seq, 'RT')
drugs = list(map(attrgetter(*compared_attrs), result.drugs))
self.assertEqual(expected_drugs, drugs)
def setUp(self):
self.asi = AsiAlgorithm(os.path.join(os.path.dirname(__file__),
"..",
"resistance",
HIV_RULES_PATH))
class AsiAlgorithmTest(TestCase):
def setUp(self):
self.asi = AsiAlgorithm(os.path.join(os.path.dirname(__file__),
"..",
"resistance",
HIV_RULES_PATH))
def test_interpret(self):
aa_seq = [[amino] for amino in self.asi.stds['RT']]
aa_seq[40] = ['L'] # Resistance mutation.
compared_attrs = ('code', 'score', 'level', 'level_name')
expected_drugs = [('3TC', 0.0, 1, 'Susceptible'),
('ABC', 5.0, 1, 'Susceptible'),
('AZT', 15.0, 3, 'Low-Level Resistance'),
('D4T', 15.0, 3, 'Low-Level Resistance'),
('DDI', 10.0, 2, 'Susceptible'),
('FTC', 0.0, 1, 'Susceptible'),
('TDF', 5.0, 1, 'Susceptible'),
('DOR', 0.0, 1, 'Susceptible'),
('EFV', 0.0, 1, 'Susceptible'),
('ETR', 0.0, 1, 'Susceptible'),
('NVP', 0.0, 1, 'Susceptible'),
('RPV', 0.0, 1, 'Susceptible')]
expected_mutation_comments = [
'M41L is a TAM that usually occurs with T215Y. In combination, '
'M41L plus T215Y confer intermediate / high-level resistance to '
'AZT and d4T and contribute to reduced ddI, ABC and TDF '
'susceptibility.']
result = self.asi.interpret(aa_seq, 'RT')
drugs = list(map(attrgetter(*compared_attrs), result.drugs))
assert expected_drugs == drugs
assert expected_mutation_comments == result.mutation_comments
def test_protease(self):
aa_seq = [[amino] for amino in self.asi.stds['PR']]
aa_seq[23] = ['I'] # Resistance mutation.
compared_attrs = ('code', 'score', 'level', 'level_name')
expected_drugs = [('ATV/r', 10.0, 2, 'Susceptible'),
('DRV/r', 0.0, 1, 'Susceptible'),
('FPV/r', 10.0, 2, 'Susceptible'),
('IDV/r', 15.0, 3, 'Low-Level Resistance'),
('LPV/r', 10.0, 2, 'Susceptible'),
('NFV', 10.0, 2, 'Susceptible'),
('SQV/r', 10.0, 2, 'Susceptible'),
('TPV/r', -5.0, 1, 'Susceptible')]
expected_mutation_comments = [
'L24I is a non-polymorphic mutation selected by IDV and LPV. It '
'contributes reduced susceptibility to each PI except DRV and TPV.']
result = self.asi.interpret(aa_seq, 'PR')
drugs = list(map(attrgetter(*compared_attrs), result.drugs))
self.assertEqual(expected_drugs, drugs)
self.assertEqual(expected_mutation_comments, result.mutation_comments)
def test_integrase(self):
aa_seq = [[amino] for amino in self.asi.stds['IN']]
aa_seq[50] = ['Y'] # Resistance mutation.
compared_attrs = ('code', 'score', 'level', 'level_name')
expected_drugs = [('BIC', 10.0, 2, 'Susceptible'),
('DTG', 10.0, 2, 'Susceptible'),
('EVG', 15.0, 3, 'Low-Level Resistance'),
('RAL', 15.0, 3, 'Low-Level Resistance')]
expected_mutation_comments = [
'H51Y is a rare non-polymorphic accessory mutation selected in '
'patients receiving RAL and EVG and in vitro by DTG. H51Y '
'minimally reduces EVG susceptibility (~2 to 3-fold). It does not '
'reduce RAL or DTG susceptibility.']
result = self.asi.interpret(aa_seq, 'IN')
drugs = list(map(attrgetter(*compared_attrs), result.drugs))
assert expected_drugs == drugs
assert expected_mutation_comments == result.mutation_comments
def test_integrase_no_coverage(self):
aa_seq = [[]] * len(self.asi.stds['IN'])
compared_attrs = ('code', 'score', 'level', 'level_name')
expected_drugs = [('BIC', 0.0, 0, 'Sequence does not meet quality-control standards'),
('DTG', 0.0, 0, 'Sequence does not meet quality-control standards'),
('EVG', 0.0, 0, 'Sequence does not meet quality-control standards'),
('RAL', 0.0, 0, 'Sequence does not meet quality-control standards')]
expected_mutation_comments = []
result = self.asi.interpret(aa_seq, 'IN')
drugs = list(map(attrgetter(*compared_attrs), result.drugs))
assert expected_drugs == drugs
assert expected_mutation_comments == result.mutation_comments
def test_comment_filter(self):
aa_seq = [[amino] for amino in self.asi.stds['PR']]
aa_seq[23] = ['D']
expected_mutation_comments = [
'L24I is a non-polymorphic mutation selected by IDV and LPV. It '
'contributes reduced susceptibility to each PI except DRV and TPV. '
'L24D is a highly unusual mutation at this position.']
result = self.asi.interpret(aa_seq, 'PR')
self.assertEqual(expected_mutation_comments, result.mutation_comments)
def test_gaps(self):
aa_seq = [{c: 1.0} for c in self.asi.stds['PR']]
aa_seq[23] = {'I': 1.0}
compared_attrs = ('code', 'score', 'level', 'level_name')
expected_drugs = [('ATV/r', 10.0, 2, 'Susceptible'),
('DRV/r', 0.0, 1, 'Susceptible'),
('FPV/r', 10.0, 2, 'Susceptible'),
('IDV/r', 15.0, 3, 'Low-Level Resistance'),
('LPV/r', 10.0, 2, 'Susceptible'),
('NFV', 10.0, 2, 'Susceptible'),
('SQV/r', 10.0, 2, 'Susceptible'),
('TPV/r', -5.0, 1, 'Susceptible')]
expected_mutation_comments = [
'L24I is a non-polymorphic mutation selected by IDV and LPV. It '
'contributes reduced susceptibility to each PI except DRV and TPV.']
result = self.asi.interpret(aa_seq, 'PR')
drugs = list(map(attrgetter(*compared_attrs), result.drugs))
self.assertEqual(expected_drugs, drugs)
self.assertEqual(expected_mutation_comments, result.mutation_comments)
def test_multiple_regions(self):
aa_seq1 = [{c: 1.0} for c in self.asi.stds['RT']]
aa_seq1[40] = {'L': 1.0}
aa_seq2 = [{c: 1.0} for c in self.asi.stds['PR']]
aa_seq2[23] = {'I': 1.0}
compared_attrs = ('code', 'score', 'level', 'level_name')
expected_drugs = [('ATV/r', 10.0, 2, 'Susceptible'),
('DRV/r', 0.0, 1, 'Susceptible'),
('FPV/r', 10.0, 2, 'Susceptible'),
('IDV/r', 15.0, 3, 'Low-Level Resistance'),
('LPV/r', 10.0, 2, 'Susceptible'),
('NFV', 10.0, 2, 'Susceptible'),
('SQV/r', 10.0, 2, 'Susceptible'),
('TPV/r', -5.0, 1, 'Susceptible')]
expected_mutation_comments = [
'L24I is a non-polymorphic mutation selected by IDV and LPV. It '
'contributes reduced susceptibility to each PI except DRV and TPV.']
self.asi.interpret(aa_seq1, 'RT')
result = self.asi.interpret(aa_seq2, 'PR')
drugs = list(map(attrgetter(*compared_attrs), result.drugs))
self.assertEqual(expected_drugs, drugs)
self.assertEqual(expected_mutation_comments, result.mutation_comments)
def test_mutations(self):
aa_seq = [[amino] for amino in self.asi.stds['RT']]
self.assertEqual(['E'], aa_seq[39])
aa_seq[39] = ['L']
self.assertEqual(['M'], aa_seq[40])
aa_seq[40] = ['L']
expected_mutations = {'NRTI': ['M41L'], 'NNRTI': []}
result = self.asi.interpret(aa_seq, 'RT')
self.assertEqual(expected_mutations, result.mutations)
def test_mutations_have_wildtype(self):
aa_seq = [[amino] for amino in self.asi.stds['RT']]
self.assertEqual(['M'], aa_seq[40])
aa_seq[40] = ['L', 'R']
expected_mutations = {'NRTI': ['M41L'], 'NNRTI': []}
result = self.asi.interpret(aa_seq, 'RT')
self.assertEqual(expected_mutations, result.mutations)
def test_drug_classes(self):
aa_seq = [[]] * 440
compared_attrs = ('code', 'name', 'drug_class')
expected_drugs = [('3TC', 'lamivudine', 'NRTI'),
('ABC', 'abacavir', 'NRTI'),
('AZT', 'zidovudine', 'NRTI'),
('D4T', 'stavudine', 'NRTI'),
('DDI', 'didanosine', 'NRTI'),
('FTC', 'emtricitabine', 'NRTI'),
('TDF', 'tenofovir', 'NRTI'),
('DOR', 'doravirine', 'NNRTI'),
('EFV', 'efavirenz', 'NNRTI'),
('ETR', 'etravirine', 'NNRTI'),
('NVP', 'nevirapine', 'NNRTI'),
('RPV', 'rilpivirine', 'NNRTI')]
result = self.asi.interpret(aa_seq, 'RT')
drugs = list(map(attrgetter(*compared_attrs), result.drugs))
self.assertEqual(expected_drugs, drugs)
def setUp(self):
self.asi = AsiAlgorithm(os.path.join(os.path.dirname(__file__),
"..",
"resistance",
"HIVDB_8.8.xml"))