How to use the goatools.anno.genetogo_reader.Gene2GoReader function in goatools

def test_anno_read():
    """Test reading an NCBI gene2go annotation file."""
    fin_anno = os.path.join(REPO, 'gene2go')
    _dnld_anno(fin_anno)
    #godag = get_godag(os.path.join(REPO, 'go-basic.obo'), loading_bar=None)

    print('\nTEST STORING ONLY ONE SPECIES')
    obj = Gene2GoReader(fin_anno)
    assert len(obj.taxid2asscs) == 1
    obj.prt_summary_anno2ev()

    print('\nTEST STORING ALL SPECIES')
    obj = Gene2GoReader(fin_anno, taxids=True)
    assert len(obj.taxid2asscs) > 1, '**EXPECTED MORE: len(taxid2asscs) == {N}'.format(
        N=len(obj.taxid2asscs))
    obj.prt_summary_anno2ev()

    print('\nTEST GETTING ASSOCIATIONS FOR ONE SPECIES')
    print("\nTEST read_ncbi_gene2go_old: [9606]")
    old_g2go_hsa = read_ncbi_gene2go_old(fin_anno, [9606])
    ## new_g2go_hsa = read_ncbi_gene2go(fin_anno, [9606])
    new_g2go_hsa = obj.get_id2gos_nss(taxids=[9606])
    assert old_g2go_hsa == new_g2go_hsa, \
      'OLD({O}) != NEW({N})'.format(O=len(old_g2go_hsa), N=len(new_g2go_hsa))
    print("\nTEST read_ncbi_gene2go_old: 9606")
    ## assert old_g2go_hsa == read_ncbi_gene2go(fin_anno, 9606)
    assert old_g2go_hsa == obj.get_id2gos_nss(taxid=9606)

    print('\nTEST GETTING REVERSE ASSOCIATIONS: GO2GENES')

def test_anno_read():
    """Test reading an NCBI gene2go annotation file."""
    fin_anno = os.path.join(REPO, 'gene2go')
    _dnld_anno(fin_anno)
    #godag = get_godag(os.path.join(REPO, 'go-basic.obo'), loading_bar=None)

    print('\nTEST STORING ONLY ONE SPECIES')
    obj = Gene2GoReader(fin_anno)
    assert len(obj.taxid2asscs) == 1
    obj.prt_summary_anno2ev()

    print('\nTEST STORING ALL SPECIES')
    obj = Gene2GoReader(fin_anno, taxids=True)
    assert len(obj.taxid2asscs) > 1, '**EXPECTED MORE: len(taxid2asscs) == {N}'.format(
        N=len(obj.taxid2asscs))
    obj.prt_summary_anno2ev()

    print('\nTEST GETTING ASSOCIATIONS FOR ONE SPECIES')
    print("\nTEST read_ncbi_gene2go_old: [9606]")
    old_g2go_hsa = read_ncbi_gene2go_old(fin_anno, [9606])
    ## new_g2go_hsa = read_ncbi_gene2go(fin_anno, [9606])
    new_g2go_hsa = obj.get_id2gos_nss(taxids=[9606])
    assert old_g2go_hsa == new_g2go_hsa, \
      'OLD({O}) != NEW({N})'.format(O=len(old_g2go_hsa), N=len(new_g2go_hsa))

#     Get http://geneontology.org/ontology/go-basic.obo
    download_go_basic_obo()

    # 1b. Download Associations, if necessary
    #     Get ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz
    fin_gene2go = download_ncbi_associations()

    # 2. Load Ontologies, Associations and Background gene set
    # 2a. Load Ontologies
    godag = GODag("go-basic.obo")

    # 2b. Load Associations for all species
    #     Read NCBI's gene2go. Store annotations in a list of namedtuples
    objanno_all = Gene2GoReader(fin_gene2go, godag=godag, taxids=True)
    objanno_mmu = Gene2GoReader(fin_gene2go, godag=godag, taxids=[10090])
    objanno_mmuhsa = Gene2GoReader(fin_gene2go, godag=godag, taxids=[10090, 9606])

    # Get associations
    # pylint: disable=bad-whitespace
    ns2assoc_all_mmu = _run_get_ns2assc(10090, objanno_all)
    ns2assoc_mmu_mmu = _run_get_ns2assc(10090, objanno_mmu)
    ns2assoc_mmuhsa_all = _run_get_ns2assc(True,  objanno_mmuhsa)
    ns2assoc_mmuhsa_mmu = _run_get_ns2assc(10090, objanno_mmuhsa)

    # Check results
    for nspc in ['BP', 'MF', 'CC']:
        assert ns2assoc_mmu_mmu[nspc] == ns2assoc_all_mmu[nspc]
        assert ns2assoc_mmu_mmu[nspc] == ns2assoc_mmuhsa_mmu[nspc]
    _chk_mmuhsa_all(objanno_mmuhsa, objanno_all, ns2assoc_mmuhsa_all)

def get_objanno(fin_anno, anno_type=None, **kws):
    """Read annotations in GAF, GPAD, Entrez gene2go, or text format."""
    # kws get_objanno: taxids hdr_only prt allow_missing_symbol
    anno_type = get_anno_desc(fin_anno, anno_type)
    if anno_type is not None:
        if anno_type == 'gene2go':
            # kws: taxid taxids
            kws_ncbi = {k:kws[k] for k in Gene2GoReader.exp_kws.intersection(kws.keys())}
            return Gene2GoReader(fin_anno, **kws_ncbi)
        if anno_type == 'gaf':
            kws_gaf = {k:kws[k] for k in GafReader.exp_kws.intersection(kws.keys())}
            return GafReader(fin_anno, **kws_gaf)
        if anno_type == 'gpad':
            kws_gpad = {k:kws[k] for k in GpadReader.exp_kws.intersection(kws.keys())}
            return GpadReader(fin_anno, **kws_gpad)
        if anno_type == 'id2gos':
            kws_id2go = {k:kws[k] for k in IdToGosReader.exp_kws.intersection(kws.keys())}
            return IdToGosReader(fin_anno, **kws_id2go)
    raise RuntimeError('UNEXPECTED ANNOTATION FILE FORMAT: {F} {D}'.format(
        F=fin_anno, D=anno_type))

def read_ncbi_gene2go(fin_gene2go, taxids=None, namespace='BP', **kws):
    """Read NCBI's gene2go. Return gene2go data for user-specified taxids."""
    print('DEPRECATED read_ncbi_gene2go: USE Gene2GoReader FROM goatools.anno.genetogo_reader')
    # pylint: disable=protected-access
    frm = sys._getframe().f_back.f_code
    print('DEPRECATED read_ncbi_gene2go CALLED FROM: {PY} BY {FNC}'.format(
        PY=frm.co_filename, FNC=frm.co_name))
    obj = Gene2GoReader(fin_gene2go, taxids=taxids)
    # By default, return id2gos. User can cause go2geneids to be returned by:
    #   >>> read_ncbi_gene2go(..., go2geneids=True
    if 'taxid2asscs' not in kws:
        if len(obj.taxid2asscs) == 1:
            taxid = next(iter(obj.taxid2asscs))
            kws_ncbi = {k:v for k, v in kws.items() if k in AnnoOptions.keys_exp}
            kws_ncbi['taxid'] = taxid
            return obj.get_id2gos(namespace, **kws_ncbi)
    # Optional detailed associations split by taxid and having both ID2GOs & GO2IDs
    # e.g., taxid2asscs = defaultdict(lambda: defaultdict(lambda: defaultdict(set))
    t2asscs_ret = obj.get_taxid2asscs(taxids, **kws)
    t2asscs_usr = kws.get('taxid2asscs', defaultdict(lambda: defaultdict(lambda: defaultdict(set))))
    if 'taxid2asscs' in kws:
        obj.fill_taxid2asscs(t2asscs_usr, t2asscs_ret)
    return obj.get_id2gos_all(t2asscs_ret)

def __init__(self, filename=None, **kws):
        # kws: taxids or taxid
        super(Gene2GoReader, self).__init__('gene2go', filename, **kws)
        # Each taxid has a list of namedtuples - one for each line in the annotations
        self.taxid2asscs = self._init_taxid2asscs()