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)
