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sumit1sensumit1sen
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adding clump finding
1 parent cf4c181 commit e6b1680

8 files changed

+119
-13
lines changed

‎.idea/bioinformaticsV2.iml

+1-1
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‎.idea/misc.xml

+1-1
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‎clumpfinding.py

+86
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‎computingfrequencies.py

+26-6
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,27 @@
11
__author__ = 'ssen'
22

33
base = 4
4+
5+
6+
def symbolToNumber(symbol):
7+
if (symbol == 'A'):
8+
coeff = 0
9+
elif symbol == 'C':
10+
coeff = 1
11+
elif symbol == 'G':
12+
coeff = 2
13+
else:
14+
coeff = 3
15+
16+
return coeff
17+
18+
19+
def patternToNumber(pattern):
20+
if len(pattern) == 0:
21+
return 0
22+
23+
return 4 * patternToNumber(pattern[0:len(pattern)-1]) + symbolToNumber(pattern[len(pattern)-1])
24+
425
def pattern_to_number(pattern):
526
# convert a string of ACGT to a number
627
numDigits = len(pattern)
@@ -27,23 +48,22 @@ def computing_frequencies(text, k):
2748

2849
for i in range(0, len(text) - k + 1):
2950
pattern = text[i:i + k]
30-
j = pattern_to_number(pattern)
51+
j = patternToNumber(pattern)
3152
frequencyArray[j] += 1
3253
return frequencyArray
3354

3455

3556
f = computing_frequencies('ACGCGGCTCTGAAA', 2)
36-
print f
37-
f = computing_frequencies('GTGTTCGCTCTTCGATCGCGGTTACACCACCTCCGGGCCGGCGGGTCAACAGTTATGGTATATCGTAGATCAAGGTGCGGCTCAGAGTTGGGACTATCGTAGTGTCGGATGAGAAGCCGACAACGCCCGGTGCGGCGGAGAAACCTAGTGGCACCTGCTATGATGATCACAGTGTGACCTTAGTTCGGGCCGTTGGGCGAACTCGCGGTGGTAAGTAACACGAGGTGGAAGGGAGACAGCTTGCTACAAAGGGCGACTTATAACACAGTTCGCAATGTGGTTCCTGGTCCATCAAGCACGGGAGTACGAAACATGACGCAACTCCCATATACTTAGCGACTGTAACCCTATGAGGTACGTTTGTGTTTAAAACGGGCTGTGTCGTAAGTCTTACACAAACCCTAGTCCTGTCAATCAAGCTGGGATGTCTGTTTGGTGGGCGCTACCACTCGGTTTTTCCGCCTAACGATTCGTCTCCGAATGATTGCTTCATTTGGCGATTCATAATCTTGCCATCGTCTTGCGACTTAAGGGTCTAAATGTGGTCTCGCGCAAGGTCGCGCGTTCCACTGACCTGGTTAGTGCGGCAAATAGAAGGTCGGACCCCCAAAGCACTTTTCTGTTATTTAAGCCGTGTACTACCGATTAACAGGGAGTGTCTTCGGAATCCTACTCGCATGGTCGATACTTTAACTTTTCCCGAGGACAAGGCAAAAGTCTTCGGAGTAAGACACACTACTCGAGCTGGGCGGACTCCACGGTACTCAGGTCATGCGTACGCTT',6)
38-
#f = computing_frequencies('ACTTCGCCTAAGTCATTTATCCCGTGGTACGACGCTCCCTTACAGTCTTATATCCCGGTATATACGCAGAAATGCCTACGTCCCCTCGTCCCACACACCAGGGAAGCTGAAATCGCTCATCTACTATGCGTGTACTTCCGGACGAAATCGTCGTCGGCTTCTGTCTGGCGCTGGAGATCCGGGCTTCTTGAGGGACACACCCATTATGACCGTTACAGGACTTACAACTACTCTGAGCAATGATGGTGCTCTGTAACGAACAAACGCACTCACCTCTGTTTCCTGTATGACATCCTCAAATGGATCGACCGTGATGTACTGAGCGAATAAGTGCGGATTACATTTATAGTCAGCTACATTTATTCGCCGCTCGGAGCAGAGTATAATGAATTTATACCACTTGTTAGACTCCTTCTCGCATTTAGCCCCTACCGCAAGTCGGAGCGTTGGGGTGCAATAGAGTTTTCAGTATCTACGTACCGTTAAGTCTCTCGCGTTCTTTCAGCAGGCATCAATATGTTGCTTGCTGTGGGGTCGGGTGGGGCGGAGAGCCAATAAAGTGCATCGGAATTGGCTGCCCTCCTACGAATCCGCAAGATGCGGTGATGCTACGTGATTATGACTACTAGCTTAGTCCC',6)
57+
print(f)
58+
#f = computing_frequencies('GTGTTCGCTCTTCGATCGCGGTTACACCACCTCCGGGCCGGCGGGTCAACAGTTATGGTATATCGTAGATCAAGGTGCGGCTCAGAGTTGGGACTATCGTAGTGTCGGATGAGAAGCCGACAACGCCCGGTGCGGCGGAGAAACCTAGTGGCACCTGCTATGATGATCACAGTGTGACCTTAGTTCGGGCCGTTGGGCGAACTCGCGGTGGTAAGTAACACGAGGTGGAAGGGAGACAGCTTGCTACAAAGGGCGACTTATAACACAGTTCGCAATGTGGTTCCTGGTCCATCAAGCACGGGAGTACGAAACATGACGCAACTCCCATATACTTAGCGACTGTAACCCTATGAGGTACGTTTGTGTTTAAAACGGGCTGTGTCGTAAGTCTTACACAAACCCTAGTCCTGTCAATCAAGCTGGGATGTCTGTTTGGTGGGCGCTACCACTCGGTTTTTCCGCCTAACGATTCGTCTCCGAATGATTGCTTCATTTGGCGATTCATAATCTTGCCATCGTCTTGCGACTTAAGGGTCTAAATGTGGTCTCGCGCAAGGTCGCGCGTTCCACTGACCTGGTTAGTGCGGCAAATAGAAGGTCGGACCCCCAAAGCACTTTTCTGTTATTTAAGCCGTGTACTACCGATTAACAGGGAGTGTCTTCGGAATCCTACTCGCATGGTCGATACTTTAACTTTTCCCGAGGACAAGGCAAAAGTCTTCGGAGTAAGACACACTACTCGAGCTGGGCGGACTCCACGGTACTCAGGTCATGCGTACGCTT',6)
59+
f = computing_frequencies('ACTTCGCCTAAGTCATTTATCCCGTGGTACGACGCTCCCTTACAGTCTTATATCCCGGTATATACGCAGAAATGCCTACGTCCCCTCGTCCCACACACCAGGGAAGCTGAAATCGCTCATCTACTATGCGTGTACTTCCGGACGAAATCGTCGTCGGCTTCTGTCTGGCGCTGGAGATCCGGGCTTCTTGAGGGACACACCCATTATGACCGTTACAGGACTTACAACTACTCTGAGCAATGATGGTGCTCTGTAACGAACAAACGCACTCACCTCTGTTTCCTGTATGACATCCTCAAATGGATCGACCGTGATGTACTGAGCGAATAAGTGCGGATTACATTTATAGTCAGCTACATTTATTCGCCGCTCGGAGCAGAGTATAATGAATTTATACCACTTGTTAGACTCCTTCTCGCATTTAGCCCCTACCGCAAGTCGGAGCGTTGGGGTGCAATAGAGTTTTCAGTATCTACGTACCGTTAAGTCTCTCGCGTTCTTTCAGCAGGCATCAATATGTTGCTTGCTGTGGGGTCGGGTGGGGCGGAGAGCCAATAAAGTGCATCGGAATTGGCTGCCCTCCTACGAATCCGCAAGATGCGGTGATGCTACGTGATTATGACTACTAGCTTAGTCCC',6)
3960
resultStr = ''
4061
for i in range(0,len(f)):
4162
if (i==0):
4263
resultStr = str(f[i])
4364
else:
4465
resultStr = resultStr + ' ' + str(f[i])
4566

46-
47-
print resultStr
67+
print(resultStr)
4868
target ='0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 2 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 2 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 1 0 1 0 0 0 0 1 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 2 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 1 0 0 0 0 1 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 1 0 1 0 0 0 0 1 0 0 1 0 1 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1 1 0 0 1 0 0 0 1 0 0 0 0 0 1 1 0 0 0 0 1 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 1 0 1 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 1 0 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 2 0 0 0 0 0 1 0 0 1 2 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 1 1 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 1 0 1 2 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 1 1 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 1 1 0 0 0 1 1 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 1 0 1 0 0 3 2 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 1 0 0 0 0 1 0 1 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 1 0 0 2 0 0 0 0 1 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 1 0 0 0 0 1 0 0 0 0 2 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 1 1 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 1 0 1 0 1 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 1 1 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 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0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 1 0 0 0 2 0 1 0 0 0 0 0 0 0 1 0 1 0 0 0 0 1 1 0 0 1 0 0 0 0 0 0 0 1 1 1 0 0 0 1 1 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 1 1 1 0 0 0 0 0 0 0 2 0 0 0 0 0 0 1 0 0 0 0 3 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1 1 0 0 0 1 0 0 0 0 1 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 1 0 0 0 1 0 1 0 0 1 0 2 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 1 0 0 1 1 0 1 0 0 0 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 1 0 0 1 0 0 0 0 0 1 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 2 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 1 1 1 0 1 0 0 2 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 1 0 1 0 0 2 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0'
4969
print (target == resultStr)

‎frequentwords.py

+1-1
Original file line numberDiff line numberDiff line change
@@ -23,4 +23,4 @@ def frequentwords(text, k):
2323
fpatterns = frequentwords(s,13)
2424
#print fpatterns
2525
fpatterns = frequentwords('CGGAGGACTCTAGGTAACGCTTATCAGGTCCATAGGACATTCA',3)
26-
print fpatterns
26+
print(fpatterns)

‎patterncount.py

+2-2
Original file line numberDiff line numberDiff line change
@@ -12,9 +12,9 @@ def pattern_count(text, pattern):
1212

1313
f=open('C:/dataset_2_6.txt')
1414
s=f.read()
15-
print s
15+
print(s)
1616
c=pattern_count(s,'CATACCGCA')
1717
#c = pattern_count('CTGTTTTTGATCCATGATATGTTATCTCTCCGTCATCAGAAGAACAGTGACGGATCGCCCTCTCTCTTGGTCAGGCGACCGTTTGCCATAATGCCCATGCTTTCCAGCCAGCTCTCAAACTCCGGTGACTCGCGCAGGTTGAGTA','CTC')
1818
#print c
1919
c = pattern_count('CGCGATACGTTACATACATGATAGACCGCGCGCGATCATATCGCGATTATC', 'CGCG')
20-
print c
20+
print(c)

‎patternmatching.py

+1-1
Original file line numberDiff line numberDiff line change
@@ -22,4 +22,4 @@ def patternmatching(pattern, genome):
2222
for i in range(0,len(indicesCombined)):
2323
a = a+' ' + str(indicesCombined[i])
2424

25-
print a
25+
print(a)

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