def testPseudomonasSymbol(self):
"""
Test to check that the output of Pseudomonas GO test files is what
we expect, and that the 'xrdb' is 'Symbol', not 'PseudoCAP'.
"""
test_ini_file = 'test_files/test_pseudomonas.ini'
go_terms = process_go.process_go_terms(test_ini_file, 'test_files/')
desired_go_term = None
for term in go_terms:
if term['title'] == 'GO-BP-0015838:amino-acid betaine transport':
desired_go_term = term
desired_go_term_info = {
'title': 'GO-BP-0015838:amino-acid betaine transport',
'abstract':
'The directed movement of betaine, the N-trimethyl derivative '
'of an amino acid, into, out of or within a cell, or between '
'cells, by means of some agent such as a transporter or pore. '
'Annotations are propagated through transitive closure as '
'recommended by the GO Consortium. Only annotations with '
'evidence coded as EXP, IDA, IPI, IMP, IGI or IEP '
'are included.',
'organism': 'Pseudomonas aeruginosa',
'xrdb': 'Symbol',
'slug': 'go0015838-pseudomonas-aeruginosa',
'annotations': {'PA3236': [19919675], 'PA5388': [19919675]}
}
self.assertEqual(desired_go_term, desired_go_term_info)
def setUp(self):
""""""
species_ini_file = 'test_files/test_human.ini'
self.kegg_sets = process_kegg.process_kegg_sets(
species_ini_file, 'test_files/')
self.go_terms = process_go.process_go_terms(
species_ini_file, 'test_files/')
self.do_terms = process_do.process_do_terms(species_ini_file)
self.main_config_file = 'test_files/test_main_config.ini'
def setUp(self):
""""""
species_ini_file = 'test_files/test_human.ini'
self.kegg_sets = process_kegg.process_kegg_sets(
species_ini_file, 'test_files/')
self.go_terms = process_go.process_go_terms(
species_ini_file, 'test_files/')
self.do_terms = process_do.process_do_terms(species_ini_file)
self.main_config_file = 'test_files/test_main_config.ini'
mc_file_parser = SafeConfigParser()
mc_file_parser.read(self.main_config_file)
tribe_url = mc_file_parser.get('Tribe parameters', 'TRIBE_URL')
secrets_file = mc_file_parser.get('main', 'SECRETS_FILE')
self.tribe_token = get_oauth_token(tribe_url, secrets_file)
def testCorrectPublications(self):
test_ini_file = 'test_files/test_zebrafish.ini'
go_terms = process_go.process_go_terms(test_ini_file, 'test_files/')
annotations = None
for term in go_terms:
if term['title'] == 'GO-BP-0009100:glycoprotein metabolic process':
annotations = term['annotations']
retrieved_annotations = {gene: set(annots) for gene, annots
in annotations.iteritems()}
desired_annotations = {
'ZDB-GENE-061110-16': set([22522421, 22522421]),
'ZDB-GENE-040315-1': set([19125692]),
'ZDB-GENE-030131-3222': set([25609749]),
'ZDB-GENE-070412-4': set([22522421]),
'ZDB-GENE-050213-1': set([21294126]),
'ZDB-GENE-020419-3': set([21294126, 22869369]),
'ZDB-GENE-030131-3127': set([22869369]),
'ZDB-GENE-121129-1': set([22869369]),
'ZDB-GENE-030131-9631': set([16188232]),
'ZDB-GENE-010102-1': set([19211552]),
'ZDB-GENE-060628-3': set([16672343]),
'ZDB-GENE-030131-5186': set([22869369]),
'ZDB-GENE-070112-1002': set([20466645]),
'ZDB-GENE-011119-1': set([21294126]),
'ZDB-GENE-040630-9': set([16156897]),
'ZDB-GENE-040724-125': set([21901110]),
'ZDB-GENE-030131-4714': set([25505245]),
'ZDB-GENE-121001-5': set([23359570]),
'ZDB-GENE-040801-234': set([23768512]),
'ZDB-GENE-041124-3': set([22869369, 15603738, 21294126]),
'ZDB-GENE-041124-2': set([22869369, 15603738]),
'ZDB-GENE-050522-358': set([23453667]),
'ZDB-GENE-111017-2': set([21901110]),
'ZDB-GENE-030722-6': set([22956764]),
'ZDB-GENE-020419-37': set([20226781, 21294126,
22869369, 20226781]),
'ZDB-GENE-070410-96': set([22522421]),
'ZDB-GENE-060929-966': set([20466645])}
self.assertEqual(retrieved_annotations, desired_annotations)
def testProcessGOTerms(self):
test_ini_file = 'test_files/test_human.ini'
go_terms = process_go.process_go_terms(test_ini_file, 'test_files/')
desired_output = [
{'abstract':
'Enables the transfer of a solute or solutes from one side of '
'a membrane to the other according to the reaction: Zn2+(out) '
'= Zn2+(in), probably powered by proton motive force. In '
'high-affinity transport the transporter is able to bind the '
'solute even if it is only present at very low concentrations.'
' Annotations are propagated through transitive closure as '
'recommended by the GO Consortium. Only annotations with '
'evidence coded as EXP, IDA, IPI, IMP, IGI or IEP are '
'included.',
'organism': 'H**o sapiens',
'annotations': {'A0A024QZP7': [], 'A0A024R216': [],
'A0A024R214': []},
'xrdb': 'UniProtKB',
'title': 'GO-BP-0000006:la liga',
'slug': 'go0000006-h**o-sapiens',
'tags': ['xi', 'omicron', 'pi']},
{'abstract':
'Catalysis of the transfer of a solute or solutes '
'from one side of a membrane to the other according to the '
'reaction: Zn2+ = Zn2+, probably powered by proton motive '
'force. In low-affinity transport the transporter is able to '
'bind the solute only if it is present at very high '
'concentrations. Annotations are propagated through transitive'
' closure as recommended by the GO Consortium. Only '
'annotations with evidence coded as EXP, IDA, IPI, IMP, IGI or'
' IEP are included.',
'organism': 'H**o sapiens',
'annotations': {'A0A024R1V6': [], 'A0A024R214': [],
'A0A024QZP7': [], 'A0A024R216': []},
'xrdb': 'UniProtKB',
'title': 'GO-BP-0000007:european team',
'slug': 'go0000007-h**o-sapiens',
'tags': ['rho', 'sigma']},
{'abstract':
"RZ - We're making this bogus term not OBSOLETE. Assists in "
"the correct assembly of ribosomes or ribosomal subunits in "
"vivo, but is not a component of the assembled ribosome when "
"performing its normal biological function. Annotations are "
"propagated through transitive closure as recommended by the "
"GO Consortium. Only annotations with evidence coded as EXP, "
"IDA, IPI, IMP, IGI or IEP are included.",
'organism': 'H**o sapiens',
'annotations': {'A0A024R214': []},
'xrdb': 'UniProtKB',
'title': 'GO-BP-0000005:premier league',
'slug': 'go0000005-h**o-sapiens',
'tags': ['lambda', 'mu', 'nu']},
{'abstract':
'The maintenance of the structure and integrity of the '
'mitochondrial genome; includes replication and segregation of'
' the mitochondrial chromosome. Annotations are propagated '
'through transitive closure as recommended by the GO '
'Consortium. Only annotations with evidence coded as EXP, '
'IDA, IPI, IMP, IGI or IEP are included.',
'organism': 'H**o sapiens',
'annotations': {'A0A024R214': []},
'xrdb': 'UniProtKB',
'title': 'GO-BP-0000002:liverpool',
'slug': 'go0000002-h**o-sapiens',
'tags': ['delta', 'epsilon', 'zeta']},
{'abstract':
'The production of new individuals that contain some portion '
'of genetic material inherited from one or more parent '
'organisms. Annotations are propagated through transitive '
'closure as recommended by the GO Consortium. Only '
'annotations with evidence coded as EXP, IDA, IPI, IMP, IGI '
'or IEP are included.',
'organism': 'H**o sapiens',
'annotations': {'A0A024QZP7': [], 'A0A024R214': []},
'xrdb': 'UniProtKB',
'title': 'GO-BP-0000003:eibar',
'slug': 'go0000003-h**o-sapiens',
'tags': ['eta', 'theta', 'iota']},
{'abstract':
'The distribution of mitochondria, including the '
'mitochondrial genome, into daughter cells after mitosis or '
'meiosis, mediated by interactions between mitochondria and '
'the cytoskeleton. Annotations are propagated through '
'transitive closure as recommended by the GO Consortium. Only'
' annotations with evidence coded as EXP, IDA, IPI, IMP, IGI '
'or IEP are included.',
'organism': 'H**o sapiens',
'annotations': {'A0A024R216': []},
'xrdb': 'UniProtKB',
'title': 'GO-BP-0000001:barcelona',
'slug': 'go0000001-h**o-sapiens',
'tags': ['alpha', 'beta', 'gamma']}
]
self.assertEqual(go_terms, desired_output)