import os, sys, numpy
dir_path = os.path.dirname(os.path.realpath(__file__))
dir_path = dir_path[:dir_path.rfind('/')] + '/0_Helper_Modules'
sys.path.insert(0, dir_path)
from DNAPatterns import DNA
DNA_STRING = sys.stdin.readline().strip()
K = sys.stdin.readline().strip()
K = int(K)
PROFILE_LINE_1 = sys.stdin.readline().strip()
PROFILE_LINE_2 = sys.stdin.readline().strip()
PROFILE_LINE_3 = sys.stdin.readline().strip()
PROFILE_LINE_4 = sys.stdin.readline().strip()
EXPECTED = sys.stdin.readline().strip()
profile = numpy.zeros([4, K])
profile[0] = PROFILE_LINE_1.split(' ')
profile[1] = PROFILE_LINE_2.split(' ')
profile[2] = PROFILE_LINE_3.split(' ')
profile[3] = PROFILE_LINE_4.split(' ')
myDNA = DNA(DNA_STRING)
kMer = myDNA.profielMostProbableKmer(K, profile)
print 'EXPECTED: ', EXPECTED
print 'GOT: ', kMer
# coding=utf-8
import os, sys
dir_path = os.path.dirname(os.path.realpath(__file__))
dir_path = dir_path[:dir_path.rfind('/')] + '/0_Helper_Modules'
sys.path.insert(0, dir_path)
from DNAPatterns import DNA
K_AND_D = sys.stdin.readline().strip() #sys.readline() les linu, strip() fjarlægir enter merki
DNAStrings = []
while True:
DNA_STRING = sys.stdin.readline().strip() #sys.readline() les linu, strip() fjarlægir enter merki
if len(DNA_STRING.split()) == 1:
DNAStrings.append(DNA(DNA_STRING))
else:
break
K = int(K_AND_D.split()[0])
D = int(K_AND_D.split()[1])
myDNA = DNA('')
allPossibleDNAStrings = myDNA.getAllPossibleKmers(K)
kMersExistInAll = []
for kMer in allPossibleDNAStrings:
wasBroken = False
for dna in DNAStrings:
doesExist = dna.kMerExistsWithMaxHammingDistance(kMer, D)
if not doesExist:
wasBroken = True
break
# coding=utf-8
import sys, os
dir_path = os.path.dirname(os.path.realpath(__file__))
dir_path = dir_path[:dir_path.rfind('/')] + '/0_Helper_Modules'
sys.path.insert(0, dir_path)
from DNAPatterns import DNA
DNA_STRING_1 = sys.stdin.readline().strip(
) #sys.readline() les linu, strip() fjarlægir enter merki
DNA_STRING_2 = sys.stdin.readline().strip(
) #sys.readline() les linu, strip() fjarlægir enter merki
myDNA = DNA(DNA_STRING_1)
print myDNA.hammingDistance(0, DNA_STRING_2)
# coding=utf-8
import sys, os
dir_path = os.path.dirname(os.path.realpath(__file__))
dir_path = dir_path[:dir_path.rfind('/')] + '/0_Helper_Modules'
sys.path.insert(0, dir_path)
from DNAPatterns import DNA
DNA_STRING = sys.stdin.readline().strip(
) #sys.readline() les linu, strip() fjarlægir enter merki
myDNAString = DNA(DNA_STRING)
print myDNAString.reverseCompliment()
# coding=utf-8
import os, sys
dir_path = os.path.dirname(os.path.realpath(__file__))
dir_path = dir_path[:dir_path.rfind('/')] + '/0_Helper_Modules'
sys.path.insert(0, dir_path)
from DNAPatterns import DNA
DNA_STRING = sys.stdin.readline().strip(
) #sys.readline() les linu, strip() fjarlægir enter merki
K_AND_D = sys.stdin.readline().strip(
) #sys.readline() les linu, strip() fjarlægir enter merki
K = int(K_AND_D.split()[0])
D = int(K_AND_D.split()[1])
myDNA = DNA(DNA_STRING)
allPossiblekMers = myDNA.getAllPossibleKmers(K)
allCounts = []
for kMer in allPossiblekMers:
allCounts.append(myDNA.howOftenkMerAppearsWithMinHammingDistance(kMer, D))
maxCount = 0
maxKMers = []
kMersCounts = dict(zip(allPossiblekMers, allCounts))
for kMer in kMersCounts:
print maxCount
if kMersCounts[kMer] > maxCount:
maxCount = kMersCounts[kMer]
maxKMers = [kMer]
elif kMersCounts[kMer] == maxCount:
maxKMers.append(kMer)
# coding=utf-8
import sys, os
dir_path = os.path.dirname(os.path.realpath(__file__))
dir_path = dir_path[:dir_path.rfind('/')] + '/0_Helper_Modules'
sys.path.insert(0, dir_path)
from DNAPatterns import DNA
PATTERN = sys.stdin.readline().strip(
) #sys.readline() les linu, strip() fjarlægir enter merki
DNA_STRING = sys.stdin.readline().strip(
) #sys.readline() les linu, strip() fjarlægir enter merki
myDNAString = DNA(DNA_STRING)
indexes = []
for i, c in enumerate(myDNAString.getString()):
if myDNAString.text(i, len(PATTERN)) == PATTERN:
indexes.append(i)
print indexes
# coding=utf-8
import sys, os
dir_path = os.path.dirname(os.path.realpath(__file__))
dir_path = dir_path[:dir_path.rfind('/')] + '/0_Helper_Modules'
sys.path.insert(0, dir_path)
from DNAPatterns import DNA
DNA_STRING = sys.stdin.readline().strip(
) #sys.readline() les linu, strip() fjarlægir enter merki
myDNA = DNA(DNA_STRING)
minSkews = myDNA.minimizeSkew(0, len(DNA_STRING))
lengths = []
for i in minSkews:
lengths.append(str(i[1]))
print ' '.join(lengths)
# coding=utf-8
import sys, os
dir_path = os.path.dirname(os.path.realpath(__file__))
dir_path = dir_path[:dir_path.rfind('/')] + '/0_Helper_Modules'
sys.path.insert(0, dir_path)
from DNAPatterns import DNA
PATTERN = sys.stdin.readline().strip(
) #sys.readline() les linu, strip() fjarlægir enter merki
DNA_STRING = sys.stdin.readline().strip(
) #sys.readline() les linu, strip() fjarlægir enter merki
MAX_DISTANCE = sys.stdin.readline().strip(
) #sys.readline() les linu, strip() fjarlægir enter merki
EXPECT = sys.stdin.readline().strip(
) #sys.readline() les linu, strip() fjarlægir enter merki
myDNA = DNA(DNA_STRING)
indices = myDNA.minHammingDistancePositions(PATTERN, int(MAX_DISTANCE))
print ' '.join(str(x) for x in indices)
print EXPECT == ' '.join(str(x) for x in indices)
print EXPECT
dir_path = os.path.dirname(os.path.realpath(__file__))
dir_path = dir_path[:dir_path.rfind('/')] + '/0_Helper_Modules'
sys.path.insert(0, dir_path)
from DNAPatterns import DNA
DNA_STRING = sys.stdin.readline().strip(
) #sys.readline() les linu, strip() fjarlægir enter merki
SOME_NUMBERS = sys.stdin.readline().strip(
) #sys.readline() les linu, strip() fjarlægir enter merki
SOME_NUMBERS = SOME_NUMBERS.split(' ')
k = int(SOME_NUMBERS[0])
L = int(SOME_NUMBERS[1])
t = int(SOME_NUMBERS[2])
myDNA = DNA(DNA_STRING)
indexes = defaultdict(list)
correctPatterns = []
for i in range((len(myDNA.getString()) - k) + 1):
pattern = myDNA.text(i, k)
indexes[pattern].append(i)
indexCount = len(indexes[pattern])
if indexCount == t:
if indexes[pattern][-1] - indexes[pattern][-t] <= L:
if pattern not in correctPatterns:
correctPatterns.append(pattern)
print correctPatterns
# coding=utf-8
import os, sys
dir_path = os.path.dirname(os.path.realpath(__file__))
dir_path = dir_path[:dir_path.rfind('/')] + '/0_Helper_Modules'
sys.path.insert(0, dir_path)
from DNAPatterns import DNA
K = sys.stdin.readline().strip(
) #sys.readline() les linu, strip() fjarlægir enter merki
K = int(K)
DNAStrings = []
for i in range(20):
DNA_STRING = sys.stdin.readline().strip(
) #sys.readline() les linu, strip() fjarlægir enter merki
if len(DNA_STRING) != 0:
DNAStrings.append(DNA(DNA_STRING))
else:
break
allPossibleKMers = DNAStrings[0].getAllPossibleKmers(K)
kMersWithMinHammingDistance = []
minTotalHammingDistance = K * len(DNAStrings)
for kMer in allPossibleKMers:
totalHammingDistance = 0
for dnaString in DNAStrings:
minHammingDistance = dnaString.minHammingDistance(kMer)
totalHammingDistance = totalHammingDistance + minHammingDistance
if totalHammingDistance < minTotalHammingDistance:
minTotalHammingDistance = totalHammingDistance
kMersWithMinHammingDistance = [kMer]