def test_has_members_er(): bpe = bp.model.getByID(uri_prefix +\ 'ProteinReference_971cec47bcd850e2b7d602f0416edacf') bpe = cast(bpc._bp('ProteinReference'), bpe) assert (bpc._has_members(bpe)) bpe = bp.model.getByID('http://identifiers.org/uniprot/P56159') bpe = cast(bpc._bp('ProteinReference'), bpe) assert (not bpc._has_members(bpe))
def test_has_members_er(): bpe = bp.model.getByID(uri_prefix +\ 'ProteinReference_971cec47bcd850e2b7d602f0416edacf') bpe = cast(bpc._bp('ProteinReference'), bpe) assert(bpc._has_members(bpe)) bpe = bp.model.getByID('http://identifiers.org/uniprot/P56159') bpe = cast(bpc._bp('ProteinReference'), bpe) assert(not bpc._has_members(bpe))
def test_get_mod_feature(): bpe = bp.model.getByID(uri_prefix +\ 'ModificationFeature_bd27a53570fb9a5094bb5929bd973217') mf = cast(bpc._bp('ModificationFeature'), bpe) mc = bpc.BiopaxProcessor._extract_mod_from_feature(mf) assert (mc[0] == 'phosphorylation') assert (mc[1] == 'T') assert (mc[2] == '274')
def test_get_mod_feature(): bpe = bp.model.getByID(uri_prefix +\ 'ModificationFeature_bd27a53570fb9a5094bb5929bd973217') mf = cast(bpc._bp('ModificationFeature'), bpe) mc = bpc.BiopaxProcessor._extract_mod_from_feature(mf) assert(mc.mod_type == 'phosphorylation') assert(mc.residue == 'T') assert(mc.position == '274')
def test_get_entity_mods(): bpe = bp.model.getByID(uri_prefix +\ 'Protein_7aeb1631f64e49491b7a0303aaaec536') protein = cast(bpc._bp('Protein'), bpe) mods = bpc.BiopaxProcessor._get_entity_mods(protein) assert(len(mods) == 5) mod_types = set([m.mod_type for m in mods]) assert(mod_types == set(['phosphorylation'])) residues = set([m.residue for m in mods]) assert(residues == set(['Y'])) mod_pos = set([m.position for m in mods]) assert(mod_pos == set(['1035', '1056', '1128', '1188', '1242']))
def test_get_entity_mods(): bpe = bp.model.getByID(uri_prefix +\ 'Protein_7aeb1631f64e49491b7a0303aaaec536') protein = cast(bpc._bp('Protein'), bpe) mods = bpc.BiopaxProcessor._get_entity_mods(protein) assert (len(mods) == 5) mod_types = set([m[0] for m in mods]) assert (mod_types == set(['phosphorylation'])) residues = set([m[1] for m in mods]) assert (residues == set(['Y'])) mod_pos = set([m[2] for m in mods]) assert (mod_pos == set(['1035', '1056', '1128', '1188', '1242']))
def test_is_complex(): bpe = bp.model.getByID('http://identifiers.org/reactome/REACT_24213.2') bpe = cast(bpc._bp('Complex'), bpe) assert (bpc._is_complex(bpe))
def test_name_uniprot_id_no_hgnc_pe(): bpe = bp.model.getByID('http://identifiers.org/reactome/REACT_27053.2') bpe = cast(bpc._bp('Protein'), bpe) name = bp._get_element_name(bpe) assert(name == 'IGHV3-13')
def test_is_er2(): bpe = bp.model.getByID(uri_prefix +\ 'ProteinReference_971cec47bcd850e2b7d602f0416edacf') bpe = cast(bpc._bp('ProteinReference'), bpe) assert (bpc._is_reference(bpe))
def test_has_members_pe2(): bpe = bp.model.getByID(uri_prefix + 'Protein_7d526475fd43d0a07ca1a596fe81aae0') bpe = cast(bpc._bp('Protein'), bpe) assert (not bpc._has_members(bpe))
def test_uniprot_id_er(): bpe = bp.model.getByID('http://identifiers.org/uniprot/Q15303') bpe = cast(bpc._bp('ProteinReference'), bpe) ids = bp._get_uniprot_id(bpe) assert ('Q15303' == ids)
def test_has_members_pe2(): bpe = bp.model.getByID(uri_prefix + 'Protein_7d526475fd43d0a07ca1a596fe81aae0') bpe = cast(bpc._bp('Protein'), bpe) assert(not bpc._has_members(bpe))
def test_has_members_pe(): bpe = bp.model.getByID('http://identifiers.org/reactome/REACT_117345.2') bpe = cast(bpc._bp('Protein'), bpe) assert(bpc._has_members(bpe))
def test_get_hgnc_id(): bpe = bp.model.getByID('http://identifiers.org/uniprot/Q15303') bpe = cast(bpc._bp('ProteinReference'), bpe) hgnc_id = bp._get_hgnc_id(bpe) assert(hgnc_id == '3432')
def test_uniprot_id_er(): bpe = bp.model.getByID('http://identifiers.org/uniprot/Q15303') bpe = cast(bpc._bp('ProteinReference'), bpe) ids = bp._get_uniprot_id(bpe) assert('Q15303' == ids)
def test_uniprot_id_pe(): bpe = bp.model.getByID('http://identifiers.org/reactome/REACT_117886.3') bpe = cast(bpc._bp('Protein'), bpe) ids = bp._get_uniprot_id(bpe) assert ('Q15303' == ids)
def test_name_uniprot_id_no_hgnc_pe(): bpe = bp.model.getByID('http://identifiers.org/reactome/REACT_27053.2') bpe = cast(bpc._bp('Protein'), bpe) name = bp._get_element_name(bpe) assert (name == 'IGHV3-13')
def test_is_er(): bpe = bp.model.getByID('http://identifiers.org/reactome/REACT_117345.2') bpe = cast(bpc._bp('Protein'), bpe) assert(not bpc._is_reference(bpe))
def test_get_hgnc_id(): bpe = bp.model.getByID('http://identifiers.org/uniprot/Q15303') bpe = cast(bpc._bp('ProteinReference'), bpe) hgnc_id = bp._get_hgnc_id(bpe) assert (hgnc_id == '3432')
def test_is_er2(): bpe = bp.model.getByID(uri_prefix +\ 'ProteinReference_971cec47bcd850e2b7d602f0416edacf') bpe = cast(bpc._bp('ProteinReference'), bpe) assert(bpc._is_reference(bpe))
def test_is_mod(): bpe = bp.model.getByID(uri_prefix +\ 'ModificationFeature_59c99eae672d2a11e971a93c7848d5c6') bpe = cast(bpc._bp('ModificationFeature'), bpe) assert(bpc._is_modification(bpe))
def test_is_mod2(): bpe = bp.model.getByID(uri_prefix +\ 'FragmentFeature_806ae27c773eb2d9138269552899c242') bpe = cast(bpc._bp('FragmentFeature'), bpe) assert(not bpc._is_modification(bpe))
def test_has_members_pe(): bpe = bp.model.getByID('http://identifiers.org/reactome/REACT_117345.2') bpe = cast(bpc._bp('Protein'), bpe) assert (bpc._has_members(bpe))
def test_is_complex(): bpe = bp.model.getByID('http://identifiers.org/reactome/REACT_24213.2') bpe = cast(bpc._bp('Complex'), bpe) assert(bpc._is_complex(bpe))
def test_is_er(): bpe = bp.model.getByID('http://identifiers.org/reactome/REACT_117345.2') bpe = cast(bpc._bp('Protein'), bpe) assert (not bpc._is_reference(bpe))
def test_is_mod2(): bpe = bp.model.getByID(uri_prefix +\ 'FragmentFeature_806ae27c773eb2d9138269552899c242') bpe = cast(bpc._bp('FragmentFeature'), bpe) assert (not bpc._is_modification(bpe))
def test_is_mod(): bpe = bp.model.getByID(uri_prefix +\ 'ModificationFeature_59c99eae672d2a11e971a93c7848d5c6') bpe = cast(bpc._bp('ModificationFeature'), bpe) assert (bpc._is_modification(bpe))
def test_uniprot_id_pe(): bpe = bp.model.getByID('http://identifiers.org/reactome/REACT_117886.3') bpe = cast(bpc._bp('Protein'), bpe) ids = bp._get_uniprot_id(bpe) assert('Q15303' == ids)