def gene_interaction_parse(cls, *args, **kwargs):
stage_output_file = cls._get_stage_output_file(*args, **kwargs)
download_file = cls._get_download_file(*args, **kwargs)
section = kwargs['section']
config = None
if 'config' in kwargs:
config = kwargs['config']
GeneInteractions.gene_interaction_parse(download_file, stage_output_file, section, config=config)
def test_interactor_json_decorator(self):
'''Test if the dict passed is returned as json with the interactor and evidence as the keys'''
json_a = GeneInteractions.interactor_json_decorator({"geneA": None})
self.assertDictEqual(json_a, {'interactor': 'geneA'}, "JSON equal for geneA")
json_b = GeneInteractions.interactor_json_decorator({"geneA": "evidenceA"})
self.assertDictEqual(json_b, {'interactor': 'geneA', 'pubmed': 'evidenceA'},
"JSON equal for geneA with evidence")
def test_group_binary_interactions(self):
'''
Test if the interactors are grouped correctly
'''
binary_interactions = [('0', '1'), ('0', '2'), ('1', '2'), ('2', '1'), ('1', '3'), ('2', '3'), ('3', '4'),
('4', '5'), ('5', '6'), ('5', '7'), ('6', '8'), ('7', '8'), ('8', '9'), ('8', '9')]
expected_dict = {
'0': [{'1': None}, {'2': None}],
'1': [{'0': None}, {'2': None}, {'3': None}],
'2': [{'0': None}, {'1': None}, {'3': None}],
'3': [{'1': None}, {'2': None}, {'4': None}],
'4': [{'3': None}, {'5': None}],
'5': [{'4': None}, {'6': None}, {'7': None}],
'6': [{'5': None}, {'8': None}],
'7': [{'5': None}, {'8': None}],
'8': [{'6': None}, {'7': None}, {'9': None}],
'9': [{'8': None}]
}
grouped_interactions = GeneInteractions._group_binary_interactions(binary_interactions)
self.assertDictEqual(grouped_interactions, expected_dict, "Grouping of interactions done OK")
self.assertTrue(10 == len(grouped_interactions), "dict contains 10 groups")
self.assertIn('8', expected_dict, "key 8 is in dict")
self.assertIn({'9': None}, grouped_interactions['8'], "value 9 is in dict['8'] ")
self.assertIn({'1': None}, grouped_interactions['0'], "value 1 is in dict['0'] ")
def test_check_binary_interactions(self):
'''Test if the grouping of the binary interactions including the evidence is working correctly'''
gene_interactors = {
'gene0': [{'gene1:evidence1'}, {'gene2:evidence2'}],
'gene1': [{'gene0:evidence0'}, {'gene2:evidence2'}, {'gene3:evidence3'}]
}
interactorA = "gene0"
interactorB = "gene4"
(gene_interactors_list_a, gene_interactors_list_b) = GeneInteractions._check_binary_interactions(gene_interactors, # @IgnorePep8
interactorA,
interactorB,
evidence_id="evidence4") # @IgnorePep8
gene_interactors[interactorA] = gene_interactors_list_a
gene_interactors[interactorB] = gene_interactors_list_b
processed_interactors1 = {'gene0': [{'gene1:evidence1'}, {'gene2:evidence2'}, {'gene4': 'evidence4'}],
'gene1': [{'gene0:evidence0'}, {'gene2:evidence2'}, {'gene3:evidence3'}],
'gene4': [{'gene0': 'evidence4'}],
}
self.assertDictEqual(gene_interactors, processed_interactors1, "Grouping OK first iteration")
interactorA = "gene4"
interactorB = "gene5"
(gene_interactors_list_a, gene_interactors_list_b) = GeneInteractions._check_binary_interactions(gene_interactors, # @IgnorePep8
interactorA,
interactorB,
evidence_id="evidence5") # @IgnorePep8
gene_interactors[interactorA] = gene_interactors_list_a
gene_interactors[interactorB] = gene_interactors_list_b
processed_interactors2 = {'gene0': [{'gene1:evidence1'}, {'gene2:evidence2'}, {'gene4': 'evidence4'}],
'gene1': [{'gene0:evidence0'}, {'gene2:evidence2'}, {'gene3:evidence3'}],
'gene4': [{'gene0': 'evidence4'}, {'gene5': 'evidence5'}],
'gene5': [{'gene4': 'evidence5'}],
}
self.assertDictEqual(gene_interactors, processed_interactors2, "Grouping OK second iteration")
def test_interaction_json_decorator(self):
'''Test if the interaction with interactors and source is returned correctly'''
json_interaction = GeneInteractions.interaction_json_decorator("intact",
"geneA",
[{"geneB": "1234"},
{"geneC": "2345"},
{"geneD": "6789"}])
self.assertIn('"_parent": "geneA"', json_interaction, "_parent found in json")
self.assertIn('"interaction_source": "intact"', json_interaction, "_parent found in json")
json_interaction = GeneInteractions.interaction_json_decorator("bioplex",
"geneA",
[{"geneB": None},
{"geneC": None},
{"geneD": None}])
self.assertJSONEqual(json_interaction,
json.dumps({"interactors": [{"interactor": "geneB"},
{"interactor": "geneC"},
{"interactor": "geneD"}],
"interaction_source": "bioplex", "_parent": "geneA"}),
"JSON for interaction equal")
def gene_interaction_parse(cls, *args, **kwargs):
stage_output_file = cls._get_stage_output_file(*args, **kwargs)
download_file = cls._get_download_file(*args, **kwargs)
section = kwargs['section']
GeneInteractions.gene_interaction_parse(download_file, stage_output_file, section)