How to use the goatools.anno.idtogos_reader.IdToGosReader function in goatools

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github tanghaibao / goatools / tests / test_yang_fig2a.py View on Github external
def _get_id2gos(file_id2gos, godag, name2go, name2num):
    """Get annotations"""
    if os.path.exists(file_id2gos):
        return IdToGosReader(file_id2gos, godag=godag).get_id2gos('CC')
    go2genes = cx.defaultdict(set)
    genenum = 0
    for name, qty in name2num.items():
        goid = name2go[name]
        for _ in range(qty):
            go2genes[goid].add(genenum)
            genenum += 1
    id2gos = get_b2aset(go2genes)
    IdToGosReader.wr_id2gos(file_id2gos, id2gos)
    return id2gos
github tanghaibao / goatools / tests / test_yang_fig2a.py View on Github external
def _get_id2gos(file_id2gos, godag, name2go, name2num):
    """Get annotations"""
    if os.path.exists(file_id2gos):
        return IdToGosReader(file_id2gos, godag=godag).get_id2gos('CC')
    go2genes = cx.defaultdict(set)
    genenum = 0
    for name, qty in name2num.items():
        goid = name2go[name]
        for _ in range(qty):
            go2genes[goid].add(genenum)
            genenum += 1
    id2gos = get_b2aset(go2genes)
    IdToGosReader.wr_id2gos(file_id2gos, id2gos)
    return id2gos
github tanghaibao / goatools / tests / test_yang_fig1b.py View on Github external
def _get_id2gos(file_id2gos, godag, name2go):
    """Get annotations"""
    if os.path.exists(file_id2gos):
        return IdToGosReader(file_id2gos, godag=godag).get_id2gos('CC')
    id2num = {
        name2go['A']:  1,
        name2go['B']:  1,
        name2go['C']: 10,
        name2go['D']: 10,
        name2go['E']: 10,
        name2go['F']: 10,
        name2go['G']: 10,
        name2go['H']: 10,
        name2go['I']: 18,
    }
    go2genes = cx.defaultdict(set)
    genenum = 0
    for goid, qty in id2num.items():
        for _ in range(qty):
            go2genes[goid].add(genenum)
github tanghaibao / goatools / tests / test_yang_fig1a.py View on Github external
def _get_id2gos(file_id2gos, godag, name2go):
    """Get annotations"""
    if os.path.exists(file_id2gos):
        return IdToGosReader(file_id2gos, godag=godag).get_id2gos('CC')
    id2num = {
        name2go['A']: 10,
        name2go['B']: 10,
        name2go['C']: 10,
        name2go['D']: 10,
        name2go['E']: 10,
        name2go['F']: 10,
        name2go['G']: 10,
        name2go['H']: 10,
        name2go['I']: 30,
        name2go['L']: 30,
        name2go['M']: 20,
        name2go['N']: 30,
    }
    go2genes = cx.defaultdict(set)
    genenum = 0
github tanghaibao / goatools / tests / test_yang_fig1b.py View on Github external
name2go['C']: 10,
        name2go['D']: 10,
        name2go['E']: 10,
        name2go['F']: 10,
        name2go['G']: 10,
        name2go['H']: 10,
        name2go['I']: 18,
    }
    go2genes = cx.defaultdict(set)
    genenum = 0
    for goid, qty in id2num.items():
        for _ in range(qty):
            go2genes[goid].add(genenum)
            genenum += 1
    id2gos = get_b2aset(go2genes)
    IdToGosReader.wr_id2gos(file_id2gos, id2gos)
    return id2gos
github tanghaibao / goatools / goatools / anno / idtogos_reader.py View on Github external
def __init__(self, filename=None, **kws):
        self.id2gos = None  # ID to GO ID set as loaded from annotations file
        super(IdToGosReader, self).__init__('id2gos', filename,
                                            godag=kws.get('godag'),
                                            namespaces=kws.get('namespaces'))
github tanghaibao / goatools / goatools / anno / factory.py View on Github external
# 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))