def test_fixedDot2ct(self):
file_path = getcwd() + sep + "Fixit"
file_path2 = getcwd() + sep + "Fixed"
title = [">mouseSeq.dot"]
title2 = [">mouseSeq.ct"]
cts = [
"GAAGUACAAUAUGUAACCG",
".(.{{((.....)))}}.."
]
cts2 = [
"1 G 0 2 0 1",
"2 A 1 3 15 2",
"3 A 2 4 0 3",
"4 G 3 5 17 4",
"5 U 4 6 16 5",
"6 A 5 7 14 6",
"7 C 6 8 13 7",
"8 A 7 9 0 8",
"9 A 8 10 0 9",
"10 U 9 11 0 10",
"11 A 10 12 0 11",
"12 U 11 13 0 12",
"13 G 12 14 7 13",
"14 U 13 15 6 14",
"15 A 14 16 2 15",
"16 A 15 17 5 16",
"17 C 16 18 4 17",
"18 C 17 19 0 18",
"19 G 18 20 0 19"
]
dot2ct(cts, title, file_path)
file_path += "(ct)"
self.assertTrue(isfile(file_path))
ct2dot(cts2, title2, file_path2)
def test_FailDot2ct(self):
file_path = getcwd() + sep + "seq-test"
title = [">mouseSeq.dot"]
cts = [
"CAGCACGACACUAGCAGUCAGUGUCAGACUGCAGACAGCACGACACUAGCAGUCAGUGUCAGACUGCAGACAGCACGACACUAGCAGUCAGUGUCAGACUGCAGA",
"..(((((...(((((...()))))...))))).....)))))...))))).."
]
dot2ct(cts, title, file_path)
file_path += "(ct)"
self.assertFalse(isfile(file_path))
def test_FailDot2ct(self):
file_path = getcwd() + sep + "seq-test"
title = [">mouseSeq.dot"]
cts = [
"CAGCACGACACUAGCAGUCAGUGUCAGACUGCAGACAGCACGACACUAGCAGUCAGUGUCAGACUGCAGACAGCACGACACUAGCAGUCAGUGUCAGACUGCAGA",
"..(((((...(((((...()))))...))))).....)))))...))))).."
]
dot2ct(cts, title, file_path)
file_path += "(ct)"
self.assertFalse(isfile(file_path))
def test_dot2ct(self):
file_path = getcwd() + sep + "seq-test"
title = [">mouseSeq.dot"]
cts = [
"CAGCACGACACUAGCAGUCAGUGUCAGACUGCAGACAGCACGACACUAGCAGUCAGUGUCAGACUGCAGACAGCACGACACUAGCAGUCAGUGUCAGACUGCAGA",
"..(((((...(((((...(((((...(((((.....)))))...))))).....(((((...(((((.....)))))...))))).....)))))...))))).."
]
file_1 = open("seq3(ct)").read()
dot2ct(cts, title, file_path)
file_path += "(ct)"
file_2 = open("seq-test(ct)").read()
self.assertTrue(isfile(file_path))
self.assertEqual(file_1, file_2)
remove(file_path)
def test_dot2ct(self):
file_path = getcwd() + sep + "seq-test"
title = [">mouseSeq.dot"]
cts = [
"CAGCACGACACUAGCAGUCAGUGUCAGACUGCAGACAGCACGACACUAGCAGUCAGUGUCAGACUGCAGACAGCACGACACUAGCAGUCAGUGUCAGACUGCAGA",
"..(((((...(((((...(((((...(((((.....)))))...))))).....(((((...(((((.....)))))...))))).....)))))...))))).."
]
file_1 = open("seq3(ct)").read()
dot2ct(cts, title, file_path)
file_path += "(ct)"
file_2 = open("seq-test(ct)").read()
self.assertTrue(isfile(file_path))
self.assertEqual(file_1, file_2)
remove(file_path)
def test_fixedDot2ct(self):
file_path = getcwd() + sep + "Fixit"
file_path2 = getcwd() + sep + "Fixed"
title = [">mouseSeq.dot"]
title2 = [">mouseSeq.ct"]
cts = ["GAAGUACAAUAUGUAACCG", ".(.{{((.....)))}}.."]
cts2 = [
"1 G 0 2 0 1", "2 A 1 3 15 2", "3 A 2 4 0 3", "4 G 3 5 17 4",
"5 U 4 6 16 5", "6 A 5 7 14 6", "7 C 6 8 13 7", "8 A 7 9 0 8",
"9 A 8 10 0 9", "10 U 9 11 0 10", "11 A 10 12 0 11",
"12 U 11 13 0 12", "13 G 12 14 7 13", "14 U 13 15 6 14",
"15 A 14 16 2 15", "16 A 15 17 5 16", "17 C 16 18 4 17",
"18 C 17 19 0 18", "19 G 18 20 0 19"
]
dot2ct(cts, title, file_path)
file_path += "(ct)"
self.assertTrue(isfile(file_path))
ct2dot(cts2, title2, file_path2)
def multil(cts, title, file_name):
dot_form = "[AUGC]{2,}"
bracket_form = "[\.\<\[\{\(\)\>\]\}\s]{2,}"
finally_form = []
dot = []
bracket = []
title = title
file_name = file_name
for x in range(0, len(cts)):
if re.match(dot_form, cts[x]):
dot.append(re.match(dot_form, cts[x]).group())
elif re.match(bracket_form, cts[x]):
bracket.append(re.match(bracket_form, cts[x]).group())
if len(dot) == len(bracket):
finally_form.append(''.join(dot))
finally_form.append(''.join(bracket))
x = input('Choose save format:' + '\n' + '0 - All formats' + '\n' +
'1 - Connect (.ct)' + '\n' + '2 - Basepair (.bpseq)' + '\n' +
'3 - RNAML (.XML)' + '\n')
try:
if x == '0':
dot2ct(finally_form, title, file_name)
dot2bpseq(finally_form, title, file_name)
dot2rnaml(finally_form, title, file_name)
elif x == '1':
dot2ct(finally_form, title, file_name)
elif x == '2':
dot2bpseq(finally_form, title, file_name)
elif x == '3':
dot2rnaml(finally_form, title, file_name)
except:
print("Invalid input format")
else:
print("Invalid input format")
elif re.match(bracket_form, file_lines[x]):
bracket.append(re.match(bracket_form, file_lines[x]).group())
for x in dot:
t = 0
while t < len(bracket):
if len(x) == len(bracket[t]):
input_form.append(x)
input_form.append(bracket[t])
t += 1
y = input('Multiline (y/n)?' + '\n')
try:
if y == 'y':
fromdot(file_lines, title, file_name)
else:
x = input(
'Choose save format:' + '\n' + '0 - All formats' + '\n' + '1 - Connect (.ct)' + '\n' + '2 - Basepair (.bpseq)' + '\n' + '3 - RNAML (.XML)' + '\n')
if x == '0':
dot2ct(input_form, title, file_name)
dot2bpseq(input_form, title, file_name)
dot2rnaml(input_form, title, file_name)
elif x == '1':
dot2ct(input_form, title, file_name)
elif x == '2':
dot2bpseq(input_form, title, file_name)
elif x == '3':
dot2rnaml(input_form, title, file_name)
except:
print("Invalid input format")
except:
print('File not found')
for x in dot:
t = 0
while t < len(bracket):
if len(x) == len(bracket[t]):
input_form.append(x)
input_form.append(bracket[t])
t += 1
y = input('Multiline (y/n)?' + '\n')
try:
if y == 'y':
multil(file_lines, title, file_name)
else:
x = input('Choose save format:' + '\n' +
'0 - All formats' + '\n' + '1 - Connect (.ct)' +
'\n' + '2 - Basepair (.bpseq)' + '\n' +
'3 - RNAML (.XML)' + '\n')
if x == '0':
dot2ct(input_form, title, file_name)
dot2bpseq(input_form, title, file_name)
dot2rnaml(input_form, title, file_name)
elif x == '1':
dot2ct(input_form, title, file_name)
elif x == '2':
dot2bpseq(input_form, title, file_name)
elif x == '3':
dot2rnaml(input_form, title, file_name)
except:
print("Invalid input format")
except:
print('File not found')