def _get_agent_node_no_bcs(agent):
node_data = _get_agent_grounding(agent)
if node_data is None:
logger.warning('Agent %s has no grounding.', agent)
return None, None
variants = []
for mod in agent.mods:
pybel_mod = pmod_namespace.get(mod.mod_type)
if not pybel_mod:
logger.info('Skipping modification of type %s on agent %s',
mod.mod_type, agent)
continue
var = pmod(namespace=pc.BEL_DEFAULT_NAMESPACE, name=pybel_mod)
if mod.residue is not None:
res = amino_acids[mod.residue]['short_name'].capitalize()
var[pc.PMOD_CODE] = res
if mod.position is not None:
var[pc.PMOD_POSITION] = int(mod.position)
variants.append(var)
for mut in agent.mutations:
var = hgvs(mut.to_hgvs())
variants.append(var)
if variants:
node_data = node_data.with_variants(variants)
if isinstance(node_data, (bioprocess, pathology)):
return node_data, None
# Also get edge data for the agent
edge_data = _get_agent_activity(agent)
return node_data, edge_data
def _get_agent_node_no_bcs(agent):
node_data = _get_agent_grounding(agent)
if node_data is None:
logger.warning('Agent %s has no grounding.', agent)
return None, None
variants = []
for mod in agent.mods:
pybel_mod = pmod_namespace.get(mod.mod_type)
if not pybel_mod:
logger.info('Skipping modification of type %s on agent %s',
mod.mod_type, agent)
continue
var = pmod(namespace=pc.BEL_DEFAULT_NAMESPACE, name=pybel_mod)
if mod.residue is not None:
res = amino_acids[mod.residue]['short_name'].capitalize()
var[pc.PMOD_CODE] = res
if mod.position is not None:
var[pc.PMOD_POSITION] = int(mod.position)
variants.append(var)
for mut in agent.mutations:
var = hgvs(mut.to_hgvs())
variants.append(var)
if variants:
node_data = node_data.with_variants(variants)
if isinstance(node_data, (bioprocess, pathology)):
return node_data, None
# Also get edge data for the agent
edge_data = _get_agent_activity(agent)
return node_data, edge_data
def _get_agent_node_no_bcs(agent):
(abundance_type, db_ns, db_id) = _get_agent_grounding(agent)
if abundance_type is None:
logger.warning('Agent %s has no grounding.', agent)
return (None, None)
node_data = {pc.FUNCTION: abundance_type,
pc.NAMESPACE: db_ns,
pc.NAME: db_id}
variants = []
for mod in agent.mods:
pybel_mod = pmod_namespace.get(mod.mod_type)
if not pybel_mod:
logger.info('Skipping modification of type %s on agent %s',
mod.mod_type, agent)
continue
var = {pc.KIND: pc.PMOD,
pc.IDENTIFIER: {
pc.NAMESPACE: pc.BEL_DEFAULT_NAMESPACE,
pc.NAME: pybel_mod}}
if mod.residue is not None:
res = amino_acids[mod.residue]['short_name'].capitalize()
var[pc.PMOD_CODE] = res
if mod.position is not None:
var[pc.PMOD_POSITION] = int(mod.position)
variants.append(var)
for mut in agent.mutations:
var = {pc.KIND: pc.HGVS, pc.IDENTIFIER: mut.to_hgvs()}
variants.append(var)
if variants:
node_data[pc.VARIANTS] = variants
# Also get edge data for the agent
edge_data = _get_agent_activity(agent)
return (node_data, edge_data)
def _get_agent_node_no_bcs(agent):
node_data = _get_agent_grounding(agent)
if node_data is None:
logger.warning('Agent %s has no grounding.', agent)
return None, None
variants = []
for mod in agent.mods:
pybel_mod = pmod_namespace.get(mod.mod_type)
if not pybel_mod:
logger.info('Skipping modification of type %s on agent %s',
mod.mod_type, agent)
continue
pmod_entity = pmod_mappings[pybel_mod]['xrefs'][0]
var = ProteinModification(
namespace=pmod_entity.namespace,
name=pmod_entity.name,
identifier=pmod_entity.identifier,
)
if mod.residue is not None:
res = amino_acids[mod.residue]['short_name'].capitalize()
var[pc.PMOD_CODE] = res
if mod.position is not None:
var[pc.PMOD_POSITION] = int(mod.position)
variants.append(var)
for mut in agent.mutations:
var = hgvs(mut.to_hgvs())
variants.append(var)
if variants and not isinstance(node_data, CentralDogma):
logger.warning('Node should not have variants: %s, %s', node_data,
variants)
elif variants:
node_data = node_data.with_variants(variants)
if isinstance(node_data, (bioprocess, pathology)):
return node_data, None
# Also get edge data for the agent
edge_data = _get_agent_activity(agent)
return node_data, edge_data
