def _stat(self, out_path, stat_path, go, goslim, out_folder, log):
log.write("Running gene_ontology.py to Retrieve GOslim terms and "
"do statistics.\n")
log.write("The following files are generated:\n")
for folder in os.listdir(out_path):
strain_stat_path = os.path.join(stat_path, folder)
self.helper.check_make_folder(strain_stat_path)
fig_path = os.path.join(strain_stat_path, "figs")
if "fig" not in os.listdir(strain_stat_path):
os.mkdir(fig_path)
stat_file = os.path.join(strain_stat_path,
"_".join(["stat", folder + ".csv"]))
map2goslim(goslim, go,
os.path.join(out_path, folder, self.all_strain),
stat_file, out_folder)
log.write("\t" + stat_file + "\n")
self.helper.move_all_content(out_folder, fig_path,
["_three_roots.png"])
self.helper.move_all_content(out_folder, fig_path,
["_molecular_function.png"])
self.helper.move_all_content(out_folder, fig_path,
["_cellular_component.png"])
self.helper.move_all_content(out_folder, fig_path,
["_biological_process.png"])
for file_ in os.listdir(fig_path):
log.write("\t" + os.path.join(fig_path, file_) + "\n")
def _stat(self, out_path, stat_path, go, goslim, out_folder, log):
log.write("Running gene_ontology.py to Retrieve GOslim terms and "
"do statistics.\n")
log.write("The following files are generated:\n")
for folder in os.listdir(out_path):
strain_stat_path = os.path.join(stat_path, folder)
self.helper.check_make_folder(strain_stat_path)
fig_path = os.path.join(strain_stat_path, "figs")
if "fig" not in os.listdir(strain_stat_path):
os.mkdir(fig_path)
stat_file = os.path.join(strain_stat_path,
"_".join(["stat", folder + ".csv"]))
map2goslim(goslim, go,
os.path.join(out_path, folder, self.all_strain),
stat_file, out_folder)
log.write("\t" + stat_file + "\n")
self.helper.move_all_content(out_folder, fig_path,
["_three_roots.png"])
self.helper.move_all_content(out_folder, fig_path,
["_molecular_function.png"])
self.helper.move_all_content(out_folder, fig_path,
["_cellular_component.png"])
self.helper.move_all_content(out_folder, fig_path,
["_biological_process.png"])
for file_ in os.listdir(fig_path):
log.write("\t" + os.path.join(fig_path, file_) + "\n")
def test_map2goslim(self):
go.plot = Mock_func().mock_plot
stat_file = os.path.join(self.test_folder, "stat.txt")
term_file = os.path.join(self.test_folder, "term.txt")
slim_file = os.path.join(self.test_folder, "slim.txt")
go_table = os.path.join(self.test_folder, "go.csv")
gen_file(term_file, self.example.obo)
gen_file(slim_file, self.example.slim)
gen_file(go_table, "aaa\t+\t150\t200\tYP_031579.1\tGO:0000003")
go.map2goslim(slim_file, term_file, go_table, stat_file, self.test_folder)
datas = import_data(stat_file)
self.assertEqual(set(datas), set(self.example.out_stat.split("\n")))
def test_map2goslim(self):
go.plot = Mock_func().mock_plot
stat_file = os.path.join(self.test_folder, "stat.txt")
term_file = os.path.join(self.test_folder, "term.txt")
slim_file = os.path.join(self.test_folder, "slim.txt")
go_table = os.path.join(self.test_folder, "go.csv")
gen_file(term_file, self.example.obo)
gen_file(slim_file, self.example.slim)
gen_file(go_table, "aaa\t+\t150\t200\tYP_031579.1\tGO:0000003")
go.map2goslim(slim_file, term_file, go_table, stat_file,
self.test_folder)
datas = import_data(stat_file)
self.assertEqual(set(datas), set(self.example.out_stat.split("\n")))
def _stat(self, out_path, stat_path, go, goslim, out_folder):
for folder in os.listdir(out_path):
strain_stat_path = os.path.join(stat_path, folder)
self.helper.check_make_folder(strain_stat_path)
fig_path = os.path.join(strain_stat_path, "figs")
if "fig" not in os.listdir(strain_stat_path):
os.mkdir(fig_path)
map2goslim(goslim, go,
os.path.join(out_path, folder, self.all_strain),
os.path.join(strain_stat_path,
"_".join(["stat", folder + ".csv"])),
out_folder)
self.helper.move_all_content(out_folder, fig_path,
["_three_roots.png"])
self.helper.move_all_content(out_folder, fig_path,
["_molecular_function.png"])
self.helper.move_all_content(out_folder, fig_path,
["_cellular_component.png"])
self.helper.move_all_content(out_folder, fig_path,
["_biological_process.png"])
def _stat(self, out_path, stat_path, go, goslim, out_folder):
for folder in os.listdir(out_path):
strain_stat_path = os.path.join(stat_path, folder)
self.helper.check_make_folder(strain_stat_path)
fig_path = os.path.join(strain_stat_path, "figs")
if "fig" not in os.listdir(strain_stat_path):
os.mkdir(fig_path)
print("Computing statistics of {0}".format(folder))
map2goslim(goslim, go,
os.path.join(out_path, folder, self.all_strain),
os.path.join(strain_stat_path,
"_".join(["stat", folder + ".csv"])),
out_folder)
self.helper.move_all_content(out_folder, fig_path,
["_three_roots.png"])
self.helper.move_all_content(out_folder, fig_path,
["_molecular_function.png"])
self.helper.move_all_content(out_folder, fig_path,
["_cellular_component.png"])
self.helper.move_all_content(out_folder, fig_path,
["_biological_process.png"])