def test_undefined_drug_within_a_drug_class(self):
"""DLV drug is missing from NNRTI drug class (the drug is associated with no drug class)"""
try:
transformer = XmlAsiTransformer(False)
fd = open(
os.path.join(
self.module_path,
"test/data/HIVDB_undefinedDrugWithinDrugClass.xml"), "r")
transformer.transform(fd)
except AsiParsingException as e:
print("testUndefinedDrugWithinADrugClass:\n\t%s" % str(e))
try:
actual_err_message = str(e).index(
"The following drugs have not been associated with a drug class"
)
except ValueError as v:
raise Exception(
"The following error message was expected: " +
"The following drugs have not been associated with a drug class\n"
+ "Instead received:%s" % (str(e)))
except Exception as exc:
print("testUndefinedDrugWithinADrugClass ex:%s" % str(exc))
raise exc
finally:
fd.close()
def test_result_out_of_range(self):
"""for ETR drug, drug class NNRTI, for the second rule, which is a boolean condition the actions contain a SCORERANGE action"""
gene_dict = dict()
transformer = None
try:
transformer = XmlAsiTransformer(False)
fd = open(
os.path.join(
self.module_path,
"test/data/HIVDB_evaluationExceptionScoreRangeAction.xml"),
"r")
gene_dict = transformer.transform(fd)
except AsiParsingException as e:
print("testInvalidRuleActionType AsiParsingException:" + str(e))
raise e
except Exception as exc:
print("testInvalidRuleActionType Exception:" + str(exc))
raise exc
gene = gene_dict.get(self.gene_name)
try:
evaluated_gene = gene.evaluate(self.mutations,
self.mutation_comparator)
except AsiEvaluationException as e:
print("No score range has been defined for a score of\n\t" +
str(e))
actual_err_message = str(e).index(
"No score range has been defined for a score of:")
assert True == (actual_err_message > -1)
def test_defined_drug_within_different_drug_classes_alg_info(self):
"""DLV drug defined in NNRTI and NRTI drug classes. Using get_algorithm_info"""
try:
transformer = XmlAsiTransformer(False)
fd = open(
os.path.join(
self.module_path,
"test/data/HIVDB_definedDrugWithinDifferentDrugClasses.xml"
), "r")
transformer.get_algorithm_info(fd)
except AsiParsingException as e:
print("testDefinedDrugWithinDifferentDrugClasses:\n\t%s" % str(e))
try:
actual_err_message = str(e).index(
"has been defined for more than one drug class")
except ValueError as v:
raise Exception(
"The following error message was expected: " +
"has been defined for more than one drug class\n" +
"Instead received:%s" % (str(e)))
except Exception as exc:
print("testDefinedDrugWithinDifferentDrugClasses ex:%s" % str(exc))
raise exc
finally:
fd.close()
def summarize_hivdb(hivdb_file):
"""Output genes and conditions covered in HIVdb XML output.
"""
res_genes = XmlAsiTransformer(True).transform(open(hivdb_file, "r"))
with open("hivdb_summary.txt", "w") as out_handle:
for gene in res_genes.values():
for drug_class in gene.get_drug_classes():
for drug in drug_class.get_drugs():
for rule in drug.get_drug_rules():
out_handle.write("%s %s %s %s\n" % (gene.name, drug_class.name,
drug.name, rule.condition.statement))
def test_float_result_rule_action_type(self):
"""for ETR drug, drug class NNRTI, for the rule, which is a score condition, the actions contain a COMMENT action"""
gene_dict = dict()
transformer = None
try:
transformer = XmlAsiTransformer(False)
fd = open(
os.path.join(
self.module_path,
"test/data/HIVDB_invalidFloatResultActionType.xml"), "r")
gene_dict = transformer.transform(fd)
except AsiParsingException as e:
print("testInvalidRuleActionType AsiParsingException:" + str(e))
raise e
except Exception as exc:
print("testInvalidRuleActionType Exception:" + str(exc))
raise exc
# get Gene
gene = gene_dict.get(self.gene_name)
# get set of DrugClass objects
drug_classes = gene.get_drug_classes()
# get DrugClass
drug_class = None
for item in drug_classes:
if item.get_class_name() == "NNRTI":
drug_class = item
break
# get Drug
drug = None
for item in drug_class.get_drugs():
if item.get_drug_name() == "ETR":
drug = item
break
# get Rule
drug_rule = drug.get_drug_rules()[0]
drug_rule.get_actions().append(
CommentAction(CommentDefinition("test", "used in Python tests",
1)))
try:
evaluated_gene = gene.evaluate(self.mutations,
self.mutation_comparator)
except AsiEvaluationException as e:
print("the action does not support a result of type:\n\t" + str(e))
actual_err_message = str(e).index(
"does not support a result of type:")
assert True == (actual_err_message > -1)
def test_drug_without_any_rule(self):
"""DLV drug does not have defined any rule"""
try:
transformer = XmlAsiTransformer(False)
fd = open(
os.path.join(self.module_path,
"test/data/HIVDB_drugWithoutAnyRule.xml"), "r")
gene_dict = transformer.transform(fd)
gene = gene_dict.get(self.gene_name)
evaluated_gene = gene.evaluate(self.mutations,
self.mutation_comparator)
print("evaluated gene:" + str(evaluated_gene))
except AsiEvaluationException as e:
print("no rules for this drug\n\t" + str(e))
raise e
except Exception as exc:
print("testDrugWtihoutAnyRule ex:" + str(exc))
raise exc
def test_missing_drug_class_name(self):
"""Test missing drug class name"""
try:
transformer = XmlAsiTransformer(self.validate_xml)
fd = open(os.path.join(self.module_path,"test/data/HIVDB_missingDrugClassName.xml"), "r")
transformer.transform(fd)
except AsiParsingException as e:
print("test_missing_drug_class_name:\n\t%s" % str(e))
try:
actual_err_message = str(e).index("Not a Stanford resistance analysis XML file")
except ValueError as v:
raise Exception("The following error message was expected: " +
"Not a Stanford resistance analysis XML file\n" +
"Instead received:%s" % (str(e)))
except Exception as exc:
print("ex:%s" % str(exc))
raise exc
finally:
fd.close()
def test_overlapping_ranges(self):
"""Test overlapping ranges"""
try:
transformer = XmlAsiTransformer(False)
fd = open(os.path.join(self.module_path,"test/data/HIVDB_overlappingRanges.xml"), "r")
transformer.transform(fd)
except AsiParsingException as e:
print("test_overLapping_ranges:\n\t%s" % str(e))
try:
actual_err_message = str(e).index("Score range values overlap")
except ValueError as v:
raise Exception("The following error message was expected: " +
"Score range values overlap\n" +
"Instead received:%s" % (str(e)))
except Exception as exc:
print("ex:%s" % str(exc))
raise exc
finally:
fd.close()
def test_missing_level_definition_sir_alg_info(self):
"""Test missing_level_definition_sir. Using get_algorithm_info"""
try:
transformer = XmlAsiTransformer(self.validate_xml)
fd = open(os.path.join(self.module_path,"test/data/HIVDB_missingLevelDefinitionSIR.xml"), "r")
transformer.get_algorithm_info(fd)
except AsiParsingException as e:
print("test_missing_level_definition_sir:\n\t%s" % str(e))
try:
actual_err_message = str(e).index("Not a Stanford resistance analysis XML file")
except ValueError as v:
raise Exception("The following error message was expected: " +
"Not a Stanford resistance analysis XML file\n" +
"Instead received:%s" % (str(e)))
except Exception as exc:
print("ex:%s" % str(exc))
raise exc
finally:
fd.close()
def test_multiple_comment_definition_tags(self):
"""Test multiple comment definition tags"""
try:
transformer = XmlAsiTransformer(self.validate_xml)
fd = open(os.path.join(self.module_path,"test/data/HIVDB_multipleCommentDefinitionTags.xml"), "r")
transformer.transform(fd)
except AsiParsingException as e:
print("test_multiple_comment_definition_tags:\n\t%s" % str(e))
try:
actual_err_message = str(e).index("Not a Stanford resistance analysis XML file")
except ValueError as v:
raise Exception("The following error message was expected: " +
"Not a Stanford resistance analysis XML file\n" +
"Instead received:%s" % (str(e)))
except Exception as exc:
print("ex:%s" % str(exc))
raise exc
finally:
fd.close()
def test_undefined_drug_alg_info(self):
"""DLV drug is not defined under a DRUG tag. Using get_algorithm_info"""
try:
transformer = XmlAsiTransformer(False)
fd = open(
os.path.join(self.module_path,
"test/data/HIVDB_undefinedDrug.xml"), "r")
transformer.get_algorithm_info(fd)
except AsiParsingException as e:
print("testUndefinedDrug\n\t" + str(e))
try:
actual_err_message = str(e).index(
"has not been defined as a drug")
except ValueError as v:
raise Exception("The following error message was expected: " +
"has not been defined as a drug\n" +
"Instead received:%s" % (str(e)))
except Exception as exc:
print("ex:" + str(exc))
raise exc
finally:
fd.close()
def test_required_global_range(self):
try:
transformer = XmlAsiTransformer(False)
fd = open(
os.path.join(self.module_path,
"test/data/HIVDB_missingRequiredGlobalRange.xml"),
"r")
transformer.transform(fd)
except AsiParsingException as e:
print(
"GLOBALRANGE tag is a required element (some rules are using USE_GLOBALRANGE tag):\n\t"
+ str(e))
try:
actual_err_message = str(e).index(
"required global range does not exist")
except ValueError as v:
raise Exception("The following error message was expected: " +
"required global range does not exist\n" +
"Instead received:%s" % (str(e)))
except Exception as exc:
print("ex:%s" % str(exc))
raise exc
finally:
fd.close()
def test_missing_required_rule_elements(self):
"""Test when a rule is missing the condition for DLV drug"""
try:
transformer = XmlAsiTransformer(self.validate_xml)
fd = open(
os.path.join(self.module_path,
"test/data/HIVDB_missingCondition.xml"), "r")
transformer.transform(fd)
except AsiParsingException as e:
print("CONDITION tag is a required element:\n\t%s" % str(e))
try:
actual_err_message = str(e).index(
"Not a Stanford resistance analysis XML file")
except ValueError as v:
raise Exception(
"The following error message was expected: " +
"Not a Stanford resistance analysis XML file\n" +
"Instead received:%s" % (str(e)))
except Exception as exc:
print("ex:%s" % str(exc))
raise exc
finally:
fd.close()
try:
transformer = XmlAsiTransformer(self.validate_xml)
fd = open(
os.path.join(self.module_path,
"test/data/HIVDB_missingActions.xml"), "r")
transformer.transform(fd)
except AsiParsingException as e:
print("ACTIONS tag is a required element:\n\t%s" % str(e))
try:
actual_err_message = str(e).index(
"Not a Stanford resistance analysis XML file")
except ValueError as v:
raise Exception(
"The following error message was expected: " +
"Not a Stanford resistance analysis XML file\n" +
"Instead received:%s" % (str(e)))
except Exception as exc:
print("ex:%s" % str(exc))
raise exc
finally:
fd.close()
def output_resistance_levels(aavf_file, xml_file, output_path):
"""
Parse aavf file to AAVF object.
Create XmlAsiTransformer.
Use transformer to evaluate drug resistance levels in the
AAVF object mutations.
Output drug resistance.
"""
records = list(parser.Reader(aavf_file).read_records())
mutations = defaultdict(list) # parse mutations from records
genes = XmlAsiTransformer(True).transform(open(xml_file, "r"))
output_file = output_path
# handles the case where the output_path was passed from somewhere
# other than to click, from the command line,
# e.g. from a test file
if isinstance(output_path, str):
output_file = open(output_path, "w+")
output_string = "#gene,drug class,drug,resistance level"
# create mutations list
for record in records:
if record.ALT[0] != "*":
mutations[record.GENE].append("%s%s" % (record.POS, record.ALT[0]))
for gene in mutations:
evaluated_gene = genes[gene].evaluate(mutations[gene],
StringMutationComparator(True))
for drug_class in evaluated_gene.get_evaluated_drug_classes():
for drug in drug_class.get_evaluated_drugs():
for condition in drug.get_evaluated_conditions():
definition = next(iter(condition.get_definitions()))
output_string += ("\n%s,%s,%s,%s" %
(gene, drug_class.get_drug_class().name,
drug.get_drug().name,
definition.get_text()))
output_file.write(output_string)
output_file.close()
return output_string
def annotate_aavf(in_file, hivdb_file, out_file):
"""Annotate an AAVF input file with drug resistance changes.
"""
res_genes = XmlAsiTransformer(True).transform(open(hivdb_file, "r"))
reader = parser.Reader(in_file)
aavf_obj = reader.read_records()
aavf_obj.infos["CAT"] = model.Info("CAT", ".", "String", "Drug resistance category", None, None)
aavf_obj.infos["DRUG"] = model.Info("DRUG", ".", "String", "Drug reistances", None, None)
with open(out_file, "w") as out_handle:
writer = parser.Writer(out_handle, aavf_obj)
for rec in aavf_obj:
if rec.POS not in rec.ALT:
rmuts = evaluate_resistance([rec], res_genes)
k = (rec.GENE, "%s%s%s" % (rec.REF, rec.POS, rec.ALT[0]))
if rmuts.get(k):
cats = []
drugs = []
for cat in rmuts.get(k).keys():
cats.append(cat)
drugs.extend(rmuts[k][cat])
rec.INFO["CAT"] = cats
rec.INFO["DRUG"] = drugs
writer.write_record(rec)
def test_bool_result_rule_action_type(self):
"""for ETR drug, drug class NNRTI, for the rule, which is a bool condition, the actions contain as SCORERANGE action"""
gene_dict = dict()
transformer = None
try:
transformer = XmlAsiTransformer(False)
fd = open(
os.path.join(self.module_path,
"test/data/HIVDB_invalidRuleActionType.xml"), "r")
gene_dict = transformer.transform(fd)
except AsiParsingException as e:
print("testInvalidRuleActionType AsiParsingException:" + str(e))
raise e
except Exception as exc:
print("testInvalidRuleActionType Exception:" + str(exc))
raise exc
try:
# get Gene
gene = gene_dict.get(self.gene_name)
# get set
drug_classes = gene.get_drug_classes()
# get DrugClass
drug_class = None
for item in drug_classes:
if item.get_class_name() == "NNRTI":
drug_class = item
break
# get Drug
drug = None
for item in drug_class.get_drugs():
if item.get_drug_name() == "ETR":
drug = item
break
levels = dict()
levels["1"] = LevelDefinition(1, "level 1", "S")
levels["2"] = LevelDefinition(1, "level 1", "S")
score_range_str = "(-INF TO 10 => 1, 11 TO INF => 2)"
score_range = transformer.parse_score_range(
score_range_str, levels)
drug_rule = drug.get_drug_rules()[0]
drug_rule.get_actions().append(ScoreRangeAction(score_range))
try:
evaluatedGene = gene.evaluate(self.mutations,
self.mutation_comparator)
except AsiEvaluationException as e:
print("the action does not support a result of type:\n\t" +
str(e))
try:
actual_err_message = str(e).index(
"does not support a result of type")
except ValueError as v:
raise Exception(
"The following error message was expected: " +
"does not support a result of type\n" +
"Instead received:%s" % (str(e)))
except AsiParsingException as ape:
print("testInvalidRuleActionType AsiParsingException (evaluate):" +
str(ape))
raise ape
