def test_plot_ppi(self):
ppi_file = os.path.join(self.test_folder, "test_ppi")
gen_file(ppi_file, self.example.ppi_file)
pp.plot_ppi(ppi_file, 0, self.test_folder, 1000)
strain = "Helicobacter pylori 26695 chromosome"
self.assertTrue(os.path.exists(
"test_folder/" + strain + "/HP0001_nusB.png"))
def test_plot_ppi(self):
ppi_file = os.path.join(self.test_folder, "test_ppi")
gen_file(ppi_file, self.example.ppi_file)
pp.plot_ppi(ppi_file, 0, self.test_folder, 1000)
strain = "Helicobacter pylori 26695 chromosome"
self.assertTrue(
os.path.exists("test_folder/" + strain + "/HP0001_nusB.png"))
def _plot(self, args_ppi, files, log):
log.write("Running plot_PPI.py to generate plots of PPI.\n")
log.write("The figures of PPI networks are generated and stored in the "
"following folders:\n")
if args_ppi.no_specific:
files["all_nospecific"].close()
files["best_nospecific"].close()
files["all_specific"].close()
files["best_specific"].close()
for folder in os.listdir(self.all_result):
if folder in os.listdir(self.fig):
print("Plotting {0}".format(folder))
out_folder_spe = os.path.join(self.fig, folder,
self.with_strain)
plot_ppi(os.path.join(self.all_result, folder,
"_".join([folder, self.with_strain + ".csv"])),
args_ppi.score, out_folder_spe, args_ppi.size)
for file_ in os.listdir(out_folder_spe):
log.write("\t" + os.path.join(
out_folder_spe, file_) + "\n")
if args_ppi.no_specific:
out_folder_nospe = os.path.join(self.fig, folder,
self.without_strain)
plot_ppi(os.path.join(self.all_result, folder,
"_".join([folder, self.without_strain + ".csv"])),
args_ppi.score, out_folder_nospe, args_ppi.size)
for file_ in os.listdir(out_folder_nospe):
log.write("\t" + os.path.join(
out_folder_nospe, file_) + "\n")
def _plot(self, args_ppi, files):
if args_ppi.no_specific:
files["all_nospecific"].close()
files["best_nospecific"].close()
files["all_specific"].close()
files["best_specific"].close()
for folder in os.listdir(self.all_result):
if folder in os.listdir(self.fig):
print("plotting {0}".format(folder))
plot_ppi(os.path.join(self.all_result, folder,
"_".join([folder, self.with_strain + ".csv"])),
args_ppi.score, os.path.join(self.fig, folder,
self.with_strain), args_ppi.size)
if args_ppi.no_specific:
plot_ppi(os.path.join(self.all_result, folder,
"_".join([folder, self.without_strain + ".csv"])),
args_ppi.score,
os.path.join(self.fig, folder,
self.without_strain), args_ppi.size)