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 bipax_model_to_sbgn(jModel):
do_layout = False # For some reason being problematic if we set this to True
jConverter = JL3ToSBGNPDConverter(None, None, do_layout)
jBaos = JByteArrayOutputStream()
output_stream = cast('java.io.OutputStream', jBaos)
# jConverter.writeSBGN method does not create the bbox objects for
# the glyphs, not sure but maybe it would be creating them if we were able
# to run it with layout enabled. Therefore, we need to jConverter.createSBGN method
# and do the rest of the work below.
jSbgn = jConverter.createSBGN(jModel)
jMap = jSbgn.getMap()
jGlyphs = jMap.getGlyph()
jGlyphs = list(jGlyphs.toArray())
assign_bbox_to_glyphs(jGlyphs)
context = JAXBContext.newInstance('org.sbgn.bindings')
marshaller = context.createMarshaller()
marshaller.setProperty(JMarshaller.JAXB_FORMATTED_OUTPUT, JBoolean(True))
marshaller.marshal(jSbgn, output_stream)
res = jBaos.toString(JStandardCharsets.UTF_8.name())
return res
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 _extract_mod_from_feature(mf):
"""Extract the type of modification and the position from
a ModificationFeature object in the INDRA format."""
# ModificationFeature / SequenceModificationVocabulary
mf_type = mf.getModificationType()
if mf_type is None:
return None
mf_type_terms = mf_type.getTerm().toArray()
known_mf_type = None
for t in mf_type_terms:
mf_type_indra = BiopaxProcessor._mftype_dict.get(t)
if mf_type_indra is None:
logger.info('Unknown modification type term: %s' % t)
else:
known_mf_type = mf_type_indra
if not known_mf_type:
logger.info('Ignored modification type %s' % mf_type_terms[0])
return None
else:
mod_type, residue = known_mf_type
# getFeatureLocation returns SequenceLocation, which is the
# generic parent class of SequenceSite and SequenceInterval.
# Here we need to cast to SequenceSite in order to get to
# the sequence position.
mf_pos = mf.getFeatureLocation()
if mf_pos is not None:
# If it is not a SequenceSite we can't handle it
if not mf_pos.modelInterface.getName() == \
'org.biopax.paxtools.model.level3.SequenceSite':
return None
mf_site = cast(_bp('SequenceSite'), mf_pos)
mf_pos_status = mf_site.getPositionStatus()
if mf_pos_status is None:
mod_pos = None
elif mf_pos_status and mf_pos_status.toString() != 'EQUAL':
logger.info('Modification site position is %s' %
mf_pos_status.toString())
else:
mod_pos = mf_site.getSequencePosition()
mod_pos = '%s' % mod_pos
else:
mod_pos = None
mc = (mod_type, residue, mod_pos)
return mc
def _extract_mod_from_feature(mf):
"""Extract the type of modification and the position from
a ModificationFeature object in the INDRA format."""
# ModificationFeature / SequenceModificationVocabulary
mf_type = mf.getModificationType()
if mf_type is None:
return None
mf_type_terms = mf_type.getTerm().toArray()
known_mf_type = None
for t in mf_type_terms:
mf_type_indra = BiopaxProcessor._mftype_dict.get(t)
if mf_type_indra is None:
logger.info('Unknown modification type term: %s' % t)
else:
known_mf_type = mf_type_indra
if not known_mf_type:
logger.info('Ignored modification type %s' % mf_type_terms[0])
return None
else:
mod_type, residue = known_mf_type
# getFeatureLocation returns SequenceLocation, which is the
# generic parent class of SequenceSite and SequenceInterval.
# Here we need to cast to SequenceSite in order to get to
# the sequence position.
mf_pos = mf.getFeatureLocation()
if mf_pos is not None:
# If it is not a SequenceSite we can't handle it
if not mf_pos.modelInterface.getName() == \
'org.biopax.paxtools.model.level3.SequenceSite':
return None
mf_site = cast(_bp('SequenceSite'), mf_pos)
mf_pos_status = mf_site.getPositionStatus()
if mf_pos_status is None:
mod_pos = None
elif mf_pos_status and mf_pos_status.toString() != 'EQUAL':
logger.info('Modification site position is %s' %
mf_pos_status.toString())
else:
mod_pos = mf_site.getSequencePosition()
else:
mod_pos = None
mc = ModCondition(mod_type, residue, mod_pos)
return mc
def _get_modification_site(self, modPE):
# Do we need to look at EntityFeatures?
modMF = [
mf for mf in modPE.getFeature().toArray()
if isinstance(mf, bpimpl('ModificationFeature'))
]
mod_pos = []
mod = []
for mf in modMF:
# ModificationFeature / SequenceModificationVocabulary
mf_type = mf.getModificationType().getTerm().toArray()[0]
if len(mf.getModificationType().getTerm().toArray()) != 1:
warnings.warn('Other than one modification term')
try:
mod_type = self._mftype_dict[mf_type]
except KeyError:
warnings.warn('Unknown modification type %s' % mf_type)
continue
mod.append(mod_type)
# getFeatureLocation returns SequenceLocation, which is the
# generic parent class of SequenceSite and SequenceInterval.
# Here we need to cast to SequenceSite in order to get to
# the sequence position.
mf_pos = mf.getFeatureLocation()
if mf_pos is not None:
mf_site = cast(bp('SequenceSite'), mf_pos)
mf_pos_status = mf_site.getPositionStatus()
if mf_pos_status and mf_pos_status.toString() != 'EQUAL':
warnings.warn('Modification site position is %s' %
mf_pos_status.toString())
mod_pos.append(mf_site.getSequencePosition())
else:
mod_pos.append(None)
# Do we need to look at mf.getFeatureLocationType()?
# It seems to be always None.
# mf_pos_type = mf.getFeatureLocationType()
return mod, mod_pos
def _get_modification_site(self, modPE):
# Do we need to look at EntityFeatures?
modMF = [mf for mf in modPE.getFeature().toArray()
if isinstance(mf, bpimpl('ModificationFeature'))]
mod_pos = []
mod = []
for mf in modMF:
# ModificationFeature / SequenceModificationVocabulary
mf_type = mf.getModificationType().getTerm().toArray()[0]
if len(mf.getModificationType().getTerm().toArray()) != 1:
warnings.warn('Other than one modification term')
try:
mod_type = self._mftype_dict[mf_type]
except KeyError:
warnings.warn('Unknown modification type %s' % mf_type)
continue
mod.append(mod_type)
# getFeatureLocation returns SequenceLocation, which is the
# generic parent class of SequenceSite and SequenceInterval.
# Here we need to cast to SequenceSite in order to get to
# the sequence position.
mf_pos = mf.getFeatureLocation()
if mf_pos is not None:
mf_site = cast(bp('SequenceSite'), mf_pos)
mf_pos_status = mf_site.getPositionStatus()
if mf_pos_status and mf_pos_status.toString() != 'EQUAL':
warnings.warn('Modification site position is %s' %
mf_pos_status.toString())
mod_pos.append(mf_site.getSequencePosition())
else:
mod_pos.append(None)
# Do we need to look at mf.getFeatureLocationType()?
# It seems to be always None.
# mf_pos_type = mf.getFeatureLocationType()
return mod, mod_pos
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_mod2():
bpe = bp.model.getByID(uri_prefix +\
'FragmentFeature_806ae27c773eb2d9138269552899c242')
bpe = cast(bpc._bp('FragmentFeature'), bpe)
assert (not bpc._is_modification(bpe))
def cast_biopax_element(bpe):
""" Casts a generic BioPAXElement object into a specific type.
This is useful when a search only returns generic elements. """
return cast(bpe.getModelInterface().getName(), 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_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 cast_biopax_element(bpe):
""" Casts a generic BioPAXElement object into a specific type.
This is useful when a search only returns generic elements. """
return cast(bpe.getModelInterface().getName(), 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_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_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_is_er2():
bpe = bp.model.getByID(uri_prefix +\
'ProteinReference_971cec47bcd850e2b7d602f0416edacf')
bpe = cast(bpc._bp('ProteinReference'), bpe)
assert (bpc._is_reference(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_complex2():
bpe = bp.model.getByID('http://identifiers.org/reactome/REACT_117345.2')
bpe = cast(bpc._bp('Protein'), bpe)
assert not bpc._is_complex(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_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_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_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_er2():
bpe = bp.model.getByID(uri_prefix +\
'ProteinReference_971cec47bcd850e2b7d602f0416edacf')
bpe = cast(bpc._bp('ProteinReference'), bpe)
assert(bpc._is_reference(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_mod():
bpe = bp.model.getByID(uri_prefix +\
'ModificationFeature_59c99eae672d2a11e971a93c7848d5c6')
bpe = cast(bpc._bp('ModificationFeature'), bpe)
assert(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_is_mod2():
bpe = bp.model.getByID(uri_prefix +\
'FragmentFeature_806ae27c773eb2d9138269552899c242')
bpe = cast(bpc._bp('FragmentFeature'), bpe)
assert(not bpc._is_modification(bpe))
