How to use the goatools.go_enrichment.GOEnrichmentStudy function in goatools

def get_goeaobj(methods=None):
    """Test GOEA with method, fdr."""
    obo_dag = GODag(ROOT + "goslim_generic.obo")
    fin_assc = ROOT + "slim_association"
    assoc = read_associations(fin_assc, 'id2gos', no_top=True)
    popul_ids = [line.rstrip() for line in open(ROOT + "small_population")]
    goeaobj = GOEnrichmentStudy(popul_ids, assoc, obo_dag, methods=methods)
    return goeaobj

def _get_results(godag, propagate_counts, relationships, prt=sys.stdout):
    """Run a GOEA. Return results"""
    taxid = 10090 # Mouse study
    geneids_pop = set(GeneID2nt_mus.keys())
    assoc_geneid2gos = get_assoc_ncbi_taxids([taxid], loading_bar=None)
    geneids_study = get_geneid2symbol("nbt.3102-S4_GeneIDs.xlsx")
    goeaobj = GOEnrichmentStudy(
        geneids_pop,
        assoc_geneid2gos,
        godag,
        propagate_counts=propagate_counts,
        relationships=relationships,
        alpha=0.05,
        methods=['fdr_bh'])
    return goeaobj.run_study(geneids_study, prt=prt)

"""Test to re-produce issue#96: Passes currently."""
    # Trying to duplicate: ValueError("All values in table must be nonnegative.
    # Get genes
    print('CWD', os.getcwd())
    study_ids = _get_geneids()
    population_ids = GENEID2NT.keys()
    # Get databases

    print(os.getcwd())
    fin = os.path.join(REPO, 'gene2go')
    dnld_ncbi_gene_file(fin, loading_bar=None)
    gene2go = read_ncbi_gene2go(fin, [9606])

    fin_obo = os.path.join(REPO, "go-basic.obo")
    godag = get_godag(fin_obo, loading_bar=None)
    goeaobj = GOEnrichmentStudy(population_ids, gene2go, godag, methods=['fdr_bh'])
    # Run GOEA Gene Ontology Enrichment Analysis
    results_goeas = goeaobj.run_study(study_ids)

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))
    # print(next(iter(results_goeas))._fields)

def _get_pvals(pvalfnc_names, prt=sys.stdout):
    fisher2pvals = {}
    taxid = 10090 # Mouse study
    file_obo = os.path.join(os.getcwd(), "go-basic.obo")
    obo_dag = get_godag(file_obo, prt, loading_bar=None)
    geneids_pop = set(GeneID2nt_mus.keys())
    assoc_geneid2gos = get_assoc_ncbi_taxids([taxid], loading_bar=None)
    geneids_study = get_geneid2symbol("nbt.3102-S4_GeneIDs.xlsx")
    for fisher in pvalfnc_names:
        goeaobj = GOEnrichmentStudy(
            geneids_pop,
            assoc_geneid2gos,
            obo_dag,
            propagate_counts=False,
            alpha=0.05,
            methods=None,
            pvalcalc=fisher)
        fisher2pvals[fisher] = goeaobj.get_pval_uncorr(geneids_study, prt)
    return fisher2pvals

def run_bonferroni():
    """Do Gene Ontology Enrichment Analysis w/Bonferroni multipletest. Print results 3 ways."""
    # ---------------------------------------------------------------------
    # Run Gene Ontology Analysis (GOEA)
    #
    # 1. Initialize
    godag = get_godag(os.path.join(os.getcwd(), "go-basic.obo"), loading_bar=None)
    fin_assc = os.path.join(REPO, "data/association")
    assoc = read_associations(fin_assc, 'id2gos', no_top=True)
    popul_ids = [line.rstrip() for line in open(os.path.join(REPO, "data/population"))]
    study_ids = [line.rstrip() for line in open(os.path.join(REPO, "data/study"))]
    # 2. Run enrichment analysis
    goea = GOEnrichmentStudy(popul_ids, assoc, godag, alpha=0.05, methods=['bonferroni'])
    results_nt = goea.run_study(study_ids)
    return results_nt, goea

def get_goea_results(method="fdr_bh"):
    """Get GOEA results."""
    root_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "data")
    obo_fin = os.path.join(root_dir, "goslim_generic.obo")
    obo_dag = GODag(obo_fin)
    fin_slim = os.path.join(root_dir, "slim_association")
    assoc = read_associations(fin_slim, 'id2gos', no_top=True)
    popul_ids = [line.rstrip() for line in open(os.path.join(root_dir, "small_population"))]
    goeaobj = GOEnrichmentStudy(popul_ids, assoc, obo_dag, methods=[method])
    study_ids = [line.rstrip() for line in open(os.path.join(root_dir, "small_study"))]
    goea_results = goeaobj.run_study(study_ids, methods=[method])
    return goea_results

def init_goea(**kws):
    """Initialize GODag and GOEnrichmentStudy."""
    godag = get_godag(os.path.join(os.getcwd(), "go-basic.obo"), loading_bar=None)
    fin_assc = ROOT + "association"
    assoc = read_associations(fin_assc, 'id2gos', no_top=True)
    popul_ids = [line.rstrip() for line in open(ROOT + "population")]
    methods = kws['methods'] if 'methods' in kws else ['not_bonferroni']
    study_ids = [line.rstrip() for line in open(ROOT + "study")]
    return GOEnrichmentStudy(popul_ids, assoc, godag, methods=methods), study_ids

def _ns2o(pop, ns2assoc, godag, propagate_counts, alpha, methods, **kws):
        return {
            ns:GOEnrichmentStudy(pop, a, godag, propagate_counts, alpha, methods, name=ns, **kws) \
                for ns, a in sorted(ns2assoc.items())}