def _compute_stat(self, args_term):
new_prefixs = []
for gff in os.listdir(self.terms["all"]):
if gff.endswith("_term_all.gff"):
out_tmp = open(self.tmps["gff"], "w")
out_tmp.write("##gff-version 3\n")
new_prefix = gff.replace("_term_all.gff", "")
new_prefixs.append(gff.replace("_term_all.gff", ""))
num = 0
fh = open(os.path.join(self.terms["all"], gff))
for entry in self.gff_parser.entries(fh):
name = '%0*d' % (5, num)
entry.attributes["ID"] = (entry.seq_id + "_terminator" +
str(num))
entry.attributes["Name"] = "_".join(["terminator_" + name])
entry.attribute_string = ";".join([
"=".join(items) for items in entry.attributes.items()
])
out_tmp.write("\t".join([
entry.info_without_attributes, entry.attribute_string
]) + "\n")
num += 1
out_tmp.close()
fh.close()
shutil.move(
self.tmps["gff"],
os.path.join(self.terms["all"],
"_".join([new_prefix, self.suffixs["gff"]])))
stat_path = os.path.join(args_term.out_folder, "statistics")
for prefix in new_prefixs:
stat_term(
os.path.join(self.terms["all"],
"_".join([prefix, self.suffixs["gff"]])),
os.path.join(self.csvs["all"],
"_".join([prefix, self.suffixs["csv"]])),
os.path.join(stat_path, "_".join(["stat", prefix + ".csv"])),
os.path.join(self.terms["best"], "_".join([prefix, "term"])),
os.path.join(self.terms["express"], "_".join([prefix,
"term"])),
os.path.join(self.terms["non"], "_".join([prefix, "term"])))
shutil.move(
os.path.join(self.terms["best"],
"_".join([prefix, self.suffixs["csv"]])),
os.path.join(self.csvs["best"],
"_".join([prefix, self.suffixs["csv"]])))
shutil.move(
os.path.join(self.terms["express"],
"_".join([prefix, self.suffixs["csv"]])),
os.path.join(self.csvs["express"],
"_".join([prefix, self.suffixs["csv"]])))
shutil.move(
os.path.join(self.terms["non"],
"_".join([prefix, self.suffixs["csv"]])),
os.path.join(self.csvs["non"],
"_".join([prefix, self.suffixs["csv"]])))
os.remove(
os.path.join(self.terms["all"],
"_".join([prefix, self.suffixs["allgff"]])))
def _compute_stat(self, args_term):
new_prefixs = []
for gff in os.listdir(self.terms["all"]):
if gff.endswith("_term_all.gff"):
out_tmp = open(self.tmps["gff"], "w")
out_tmp.write("##gff-version 3\n")
new_prefix = gff.replace("_term_all.gff", "")
new_prefixs.append(gff.replace("_term_all.gff", ""))
num = 0
fh = open(os.path.join(self.terms["all"], gff))
for entry in self.gff_parser.entries(fh):
name = '%0*d' % (5, num)
entry.attributes["ID"] = "term" + str(num)
entry.attributes["Name"] = "_".join(["Terminator_" + name])
entry.attribute_string = ";".join([
"=".join(items) for items in entry.attributes.items()])
out_tmp.write("\t".join([entry.info_without_attributes,
entry.attribute_string]) + "\n")
num += 1
out_tmp.close()
fh.close()
shutil.move(self.tmps["gff"], os.path.join(self.terms["all"],
"_".join([new_prefix, self.suffixs["gff"]])))
if args_term.stat:
stat_path = os.path.join(args_term.out_folder, "statistics")
for prefix in new_prefixs:
stat_term(os.path.join(self.terms["all"],
"_".join([prefix, self.suffixs["gff"]])),
os.path.join(self.csvs["all"],
"_".join([prefix, self.suffixs["csv"]])),
os.path.join(stat_path,
"_".join(["stat", prefix + ".csv"])),
os.path.join(self.terms["best"],
"_".join([prefix, "term"])),
os.path.join(self.terms["express"],
"_".join([prefix, "term"])),
os.path.join(self.terms["non"],
"_".join([prefix, "term"])))
shutil.move(os.path.join(self.terms["best"],
"_".join([prefix, self.suffixs["csv"]])),
os.path.join(self.csvs["best"],
"_".join([prefix, self.suffixs["csv"]])))
shutil.move(os.path.join(self.terms["express"],
"_".join([prefix, self.suffixs["csv"]])),
os.path.join(self.csvs["express"],
"_".join([prefix, self.suffixs["csv"]])))
shutil.move(os.path.join(self.terms["non"],
"_".join([prefix, self.suffixs["csv"]])),
os.path.join(self.csvs["non"],
"_".join([prefix, self.suffixs["csv"]])))
os.remove(os.path.join(self.terms["all"],
"_".join([prefix, self.suffixs["allgff"]])))
def test_stat_term(self):
term_gff = os.path.join(self.test_folder, "aaa_term.gff")
term_table = os.path.join(self.test_folder, "aaa_term.csv")
stat = os.path.join(self.test_folder, "stat")
output_decrease = os.path.join(self.test_folder, "decrease")
output_expression = os.path.join(self.test_folder, "expression")
output_non = os.path.join(self.test_folder, "non_expressed")
gen_file(term_gff, self.example.gff)
gen_file(term_table, self.example.table)
st.stat_term(term_gff, term_table, stat, output_decrease, output_expression, output_non)
self.assertTrue(stat)
datas = import_data(output_decrease + ".csv")
self.assertEqual("\n".join(datas), self.example.table)
datas = import_data(output_expression + ".csv")
self.assertEqual("\n".join(datas), self.example.table)
def test_stat_term(self):
term_gff = os.path.join(self.test_folder, "aaa_term.gff")
term_table = os.path.join(self.test_folder, "aaa_term.csv")
stat = os.path.join(self.test_folder, "stat")
output_decrease = os.path.join(self.test_folder, "decrease")
output_expression = os.path.join(self.test_folder, "expression")
output_non = os.path.join(self.test_folder, "non_expressed")
gen_file(term_gff, self.example.gff)
gen_file(term_table, self.example.table)
st.stat_term(term_gff, term_table, stat, output_decrease, output_expression, output_non)
self.assertTrue(stat)
datas = import_data(output_decrease + ".csv")
self.assertEqual("\n".join(datas), self.example.table)
datas = import_data(output_expression + ".csv")
self.assertEqual("\n".join(datas), self.example.table)