def main():
pathway1 = "R-HSA-9613829" # Regulation of glycolysis by fructose 2,6-bisphosphate metabolism
os.chdir(os.path.dirname(os.path.abspath(sys.executable)) + "\\..\\..")
print(f"Working directory: {os.getcwd()}")
g = create_pathway_interaction_network(pathway1, proteoforms,
with_unique_sm,
"resources/pathway_networks/")
# Calculate articulation points
list()
# Calculate bridges
# Mark edges
# Update the graph file
p = plot_interaction_network(
g,
coloring=Coloring.ENTITY_TYPE,
plot_width=600,
plot_height=500,
title="Test Plot Bridges and Articulation Points",
legend_location="right")
show(p)
print("Finished")
def main():
pathway1 = "R-HSA-8876725"
os.chdir(os.path.dirname(os.path.abspath(sys.executable)) + "\\..\\..")
print(os.getcwd())
g = create_pathway_interaction_network(pathway1, config.proteoforms,
config.with_unique_sm,
"resources/pathway_networks/")
p = plot_interaction_network(g,
coloring=Coloring.ENTITY_TYPE,
plot_width=600,
plot_height=500,
title="Test title",
legend_location="right")
graphs = create_pathway_interaction_networks(
pathway1, "resources/pathway_networks/")
p = plot_pathway_all_levels(pathway1,
out_path="resources/pathway_networks/",
graphs=graphs,
coloring=Coloring.ENTITY_TYPE,
outline_line_width=1,
node_size=12,
inner_plot_size=350,
highlight_articulations=True,
highlight_bridges=True,
toolbar_location=None)
show(p)
def glycolysis_graph(tmpdir_factory):
# Pathway "Regulation of glycolysis by fructose" R-HSA-9634600
graphs_path = tmpdir_factory.mktemp("tmpdir")
return create_pathway_interaction_network("R-HSA-9634600", proteoforms,
with_sm, graphs_path)
def signal_graph(tmpdir_factory):
# Pathway "FRS-mediated FGFR3 signaling" R-HSA-5654706
graphs_path = tmpdir_factory.mktemp("tmpdir")
return create_pathway_interaction_network("R-HSA-5654706", proteoforms,
with_sm, graphs_path)
def traffic_graph(tmpdir_factory):
# Pathway "RHO sm_GTPases regulate P13569 trafficking" R-HSA-5627083
graphs_path = tmpdir_factory.mktemp("tmpdir")
return create_pathway_interaction_network("R-HSA-5627083", proteoforms,
with_sm, graphs_path)
def test_create_graph_wrong_level_raises_exception():
with pytest.raises(Exception):
create_pathway_interaction_network("R-HSA-9634600", "banana", no_sm)
def pathway_free_fatty_acid_receptors(tmpdir_factory):
# Pathway "Free fatty acid receptors" R-HSA-444209
graphs_path = tmpdir_factory.mktemp("tmpdir")
return create_pathway_interaction_network("R-HSA-444209", genes, with_sm,
graphs_path)
def PI_3K_cascade_FGFR3_graph_with_unique_sm(tmpdir_factory):
# Pathway "PI-3K cascade:FGFR3" R-HSA-5654710
graphs_path = tmpdir_factory.mktemp("tmpdir")
g = create_pathway_interaction_network("R-HSA-5654710", proteoforms,
with_unique_sm, graphs_path)
return g
