def test_i122():
"""Test to re-produce issue#122: Passes currently."""
obj = _Run(9606, 'gene2go', 'go-basic.obo')
study_ids, population_ids = obj.get_genes_study_n_bg()
# Result is the same whether fisher_scipy_stats of fisher
pvalcalc = 'fisher_scipy_stats'
goeaobj = GOEnrichmentStudy(population_ids,
obj.gene2go,
obj.godag,
methods=['bonferroni', 'fdr_bh'],
pvalcalc=pvalcalc)
# Run GOEA Gene Ontology Enrichment Analysis
results_goeas = goeaobj.run_study_nts(study_ids)
print(
'NS GO p stu_ratio pop_ratio p-uncorr bonferro fdr_bh stu '
)
for ntd in results_goeas:
if ntd.study_count == 0:
doprt = False
if ntd.p_bonferroni < 0.05:
assert ntd.enrichment == 'p'
doprt = True
if ntd.p_fdr_bh < 0.05:
assert ntd.enrichment == 'p'
doprt = True
if doprt:
print(obj.str_nt(ntd))
def test_i122():
"""Test to re-produce issue#122: Passes currently."""
obj = _Run(9606, 'gene2go', 'go-basic.obo')
study_ids, population_ids = obj.get_genes_study_n_bg()
# Result is the same whether fisher_scipy_stats of fisher
pvalcalc = 'fisher_scipy_stats'
goeaobj = GOEnrichmentStudy(population_ids, obj.gene2go, obj.godag, methods=['bonferroni', 'fdr_bh'], pvalcalc=pvalcalc)
# Run GOEA Gene Ontology Enrichment Analysis
results_goeas = goeaobj.run_study_nts(study_ids)
print('NS GO p stu_ratio pop_ratio p-uncorr bonferro fdr_bh stu ')
for ntd in results_goeas:
if ntd.study_count == 0:
doprt = False
if ntd.p_bonferroni < 0.05:
assert ntd.enrichment == 'p'
doprt = True
if ntd.p_fdr_bh < 0.05:
assert ntd.enrichment == 'p'
doprt = True
if doprt:
print(obj.str_nt(ntd))
