How to use the goatools.test_data.nature3102_goea.get_geneid2symbol function in goatools

def test_example():
    """Run Gene Ontology Enrichment Analysis (GOEA) on Nature data."""
    # --------------------------------------------------------------------
    # --------------------------------------------------------------------
    # Gene Ontology Enrichment Analysis (GOEA)
    # --------------------------------------------------------------------
    # --------------------------------------------------------------------
    taxid = 10090 # Mouse study
    # Load ontologies, associations, and population ids
    geneids_pop = GeneID2nt_mus.keys()
    geneids2symbol_study = get_geneid2symbol("nbt.3102-S4_GeneIDs.xlsx")
    geneids_study = geneids2symbol_study.keys()
    goeaobj = get_goeaobj("fdr_bh", geneids_pop, taxid)
    # Run GOEA on study
    goea_results_all = goeaobj.run_study(geneids_study)
    goea_results_sig = [r for r in goea_results_all if r.p_fdr_bh < 0.05]
    goea_results_sub = [r for r in goea_results_sig if r.study_count > r.study_n/10]
    # Print GOEA results to files: With study genes printed as geneids or symbols
    goeaobj.wr_xlsx("nbt3102_symbols.xlsx", goea_results_sub, itemid2name=geneids2symbol_study)
    goeaobj.wr_xlsx("nbt3102_geneids.xlsx", goea_results_sub)

def test_example(log=sys.stdout):
    """Run Gene Ontology Enrichment Analysis (GOEA) on Nature data."""
    # --------------------------------------------------------------------
    # --------------------------------------------------------------------
    # Gene Ontology Enrichment Analysis (GOEA)
    # --------------------------------------------------------------------
    # --------------------------------------------------------------------
    taxid = 10090 # Mouse study
    # Load ontologies, associations, and population ids
    geneids_pop = GeneID2nt_mus.keys()
    geneids_study = get_geneid2symbol("nbt.3102-S4_GeneIDs.xlsx")
    goeaobj = get_goeaobj("fdr_bh", geneids_pop, taxid)
    # Run GOEA on study
    #keep_if = lambda nt: getattr(nt, "p_fdr_bh" ) < 0.05 # keep if results are significant
    goea_results_all = goeaobj.run_study(geneids_study)
    goea_results_sig = [r for r in goea_results_all if r.p_fdr_bh < 0.05]
    compare_results(goea_results_all)
    geneids = get_study_items(goea_results_sig)
    # Print GOEA results to files
    goeaobj.wr_xlsx("nbt3102.xlsx", goea_results_sig)
    goeaobj.wr_txt("nbt3102_sig.txt", goea_results_sig)
    goeaobj.wr_txt("nbt3102_all.txt", goea_results_all)
    # Plot all significant GO terms w/annotated study info (large plots)
    #plot_results("nbt3102_{NS}.png", goea_results_sig)
    #plot_results("nbt3102_{NS}_sym.png", goea_results_sig, study_items=5, items_p_line=2, id2symbol=geneids_study)

def test_example():
    """Run Gene Ontology Enrichment Analysis (GOEA) on Nature data."""
    # --------------------------------------------------------------------
    # --------------------------------------------------------------------
    # Gene Ontology Enrichment Analysis (GOEA)
    # --------------------------------------------------------------------
    # --------------------------------------------------------------------
    taxid = 10090 # Mouse study
    # Load ontologies, associations, and population ids
    geneids_pop = GeneID2nt_mus.keys()
    geneids2symbol_study = get_geneid2symbol("nbt.3102-S4_GeneIDs.xlsx")
    geneids_study = geneids2symbol_study.keys()
    goeaobj = get_goeaobj("fdr_bh", geneids_pop, taxid)
    # Run GOEA on study
    goea_results_all = goeaobj.run_study(geneids_study)
    goea_results_sig = [r for r in goea_results_all if r.p_fdr_bh < 0.05]
    # Print GOEA results to files: With study genes printed as geneids or symbols
    goeaobj.wr_xlsx("nbt3102_sig_symbols.xlsx", goea_results_sig, itemid2name=geneids2symbol_study)
    goeaobj.wr_xlsx("nbt3102_sig_geneids.xlsx", goea_results_sig)
    goeaobj.wr_xlsx("nbt3102_all_symbols.xlsx", goea_results_all, itemid2name=geneids2symbol_study)
    goeaobj.wr_xlsx("nbt3102_all_geneids.xlsx", goea_results_all)

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 test_example():
    """Test GoeaPrintFunctions::print_results."""
    # --------------------------------------------------------------------
    # --------------------------------------------------------------------
    # Gene Ontology Enrichment Analysis (GOEA)
    # --------------------------------------------------------------------
    # --------------------------------------------------------------------
    taxid = 10090 # Mouse study
    # Load ontologies, associations, and population ids
    geneids_pop = GeneID2nt_mus.keys()
    geneids2symbol_study = get_geneid2symbol("nbt.3102-S4_GeneIDs.xlsx")
    geneids_study = geneids2symbol_study.keys()
    goeaobj = get_goeaobj("fdr_bh", geneids_pop, taxid)
    # Run GOEA on study
    goea_results_all = goeaobj.run_study(geneids_study)
    goea_results_sig = [r for r in goea_results_all if r.p_fdr_bh < 0.05]
    #goea_results_nt = MgrNtGOEAs(goea_results_sig).get_goea_nts_all()
    objprtres = GoeaPrintFunctions()
    objprtres.print_results(goea_results_sig)
    objprtres.print_date()

def test_example():
    """Test GoeaResults in plotting package."""
    # --------------------------------------------------------------------
    # --------------------------------------------------------------------
    # Gene Ontology Enrichment Analysis (GOEA)
    # --------------------------------------------------------------------
    # --------------------------------------------------------------------
    taxid = 10090 # Mouse study
    # Load ontologies, associations, and population ids
    geneids_pop = GeneID2nt_mus.keys()
    geneids2symbol_study = get_geneid2symbol("nbt.3102-S4_GeneIDs.xlsx")
    geneids_study = geneids2symbol_study.keys()
    goeaobj = get_goeaobj("fdr_bh", geneids_pop, taxid)
    go2obj = goeaobj.obo_dag
    # Run GOEA on study
    goea_results_all = goeaobj.run_study(geneids_study)
    goea_results_sig = [r for r in goea_results_all if r.p_fdr_bh < 0.05]
    goea_results_nt = MgrNtGOEAs(goea_results_sig).get_goea_nts_all()
    assert goea_results_nt
    ns2gos = get_ns2gos(goea_results_sig)
    # Test plotting GOEA results
    gosubdag = GoSubDag(set(r.GO for r in goea_results_sig), go2obj)
    plot_results("test_plot_goids_a_goea_{NS}.png", goea_results_sig,
                 id2symbol=geneids2symbol_study, parentcnt=True, childcnt=True)
    for nss, goids in ns2gos.items():
        plt_goids(gosubdag, "test_plot_goids_b_{NS}.png".format(NS=nss), goids)
        plot_gos("test_plot_goids_c_{NS}.png".format(NS=nss), goids, go2obj)

def test_example():
    """Test GoeaPrintFunctions::print_results."""
    # --------------------------------------------------------------------
    # --------------------------------------------------------------------
    # Gene Ontology Enrichment Analysis (GOEA)
    # --------------------------------------------------------------------
    # --------------------------------------------------------------------
    taxid = 10090 # Mouse study
    # Load ontologies, associations, and population ids
    geneids_pop = GeneID2nt_mus.keys()
    geneids2symbol_study = get_geneid2symbol("nbt.3102-S4_GeneIDs.xlsx")
    goeaobj = get_goeaobj("fdr_bh", geneids_pop, taxid)
    # No study genes at all
    geneids_study_none = set()
    goea_results_all = goeaobj.run_study(geneids_study_none)
    assert not goea_results_all, 'NO STUDY GENES TEST FAILED: {R}'.format(R=goea_results_all)
    # No study genes in population or association
    geneids_study_bad = set(['BADVAL'])
    goea_results_all = goeaobj.run_study(geneids_study_bad)
    # goea_results_sig = [r for r in goea_results_all if r.p_fdr_bh < 0.05]
    assert not goea_results_all, 'NO VALID STUDY GENES TEST FAILED: {R}'.format(R=goea_results_all)
    # goea_results_all = goeaobj.run_study(geneids_study)
    objprtres = GoeaPrintFunctions()
    objprtres.print_results(goea_results_all, pval=None)
    objprtres.print_date()

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)