def _match_disease(v: Vertex) -> bool:
"""Tests if a vertex name matches the regular expression for disease ids."""
try:
disease_regex.match(v.attributes()["name"])
except TypeError:
print(v.attributes()["name"])
print(type(v.attributes()["name"]))
sys.exit()
return bool(disease_regex.match(v.attributes()["name"]))
def get_for(cls, v: Vertex, decompiler: 'ExplorerScriptSsbDecompiler',
parent: AbstractWriteHandler,
vertex_that_started_block: Vertex,
is_first_vertex_of_block: bool) -> AbstractWriteHandler:
from explorerscript.ssb_converting.decompiler.write_handlers.foreign_label import ForeignLabelWriteHandler
from explorerscript.ssb_converting.decompiler.write_handlers.label import LabelWriteHandler
from explorerscript.ssb_converting.decompiler.write_handlers.label_jump import LabelJumpWriteHandler
from explorerscript.ssb_converting.decompiler.write_handlers.simple_op import SimpleOperationWriteHandler
if 'op' not in v.attributes():
raise ValueError(f"Invalid Ssb vertex: {v}")
op: SsbOperation = v['op']
if isinstance(op, SsbLabel):
return LabelWriteHandler(v, decompiler, parent,
vertex_that_started_block,
is_first_vertex_of_block)
if isinstance(op, SsbForeignLabel):
return ForeignLabelWriteHandler(v, decompiler, parent,
vertex_that_started_block,
is_first_vertex_of_block)
if isinstance(op, SsbLabelJump):
return LabelJumpWriteHandler(v, decompiler, parent)
return SimpleOperationWriteHandler(v, decompiler, parent)
def _is_significantly_differentiated(self, v: Vertex) -> bool:
"""In a heterogeneous network, the vertex has to be tested if it is a gene before testing if it's up or
down regulated."""
return self.is_gene(v) and v.attributes()['padj'] < self.max_adj_p
def _match_drug(v: Vertex) -> bool:
"""Tests if a vertex name matches the regular expression for Drugbank ids. """
return bool(drugbank_regex.match(v.attributes()["name"]))
def is_disease(v: Vertex) -> bool:
"""Tests if a vertex is a disease node. """
return v.attributes()['type'] == 'disease'
def is_gene(v: Vertex) -> bool:
"""Tests if a vertex is a gene node. """
return v.attributes()['type'] == 'gene'
def is_drug(v: Vertex) -> bool:
"""Tests if a vertex is a drug node. """
return v.attributes()['type'] == 'drug'
def _is_downregulated_gene(self, v: Vertex) -> bool:
return self._is_significantly_differentiated(
v) and v.attributes()['l2fc'] < self.max_l2fc
def _is_significantly_differentiated(self, v: Vertex) -> bool:
return v.attributes()['padj'] < self.max_adj_p