def letter_Look_Ahead(D, P_of_Occur, count_Threshold) :
D2 = {}
word_Array = []
hold_Array = dictionaryToArrays.dictionary_To_Arrays(D)
word_Array = hold_Array[0]
letter_Array = ['A', 'C', 'G', 'T']
weighted_Prob_Array = [len(D['A']), len(D['C']), len(D['G']), len(D['T'])]
sum_Prob = float(weighted_Prob_Array[0] + weighted_Prob_Array[1] + weighted_Prob_Array[2] + weighted_Prob_Array[3])
weighted_Prob_Array[0] = weighted_Prob_Array[0] / float(sum_Prob)
weighted_Prob_Array[1] = weighted_Prob_Array[1] / float(sum_Prob)
weighted_Prob_Array[2] = weighted_Prob_Array[2] / float(sum_Prob)
weighted_Prob_Array[3] = weighted_Prob_Array[3] / float(sum_Prob)
print weighted_Prob_Array
print '^'
grown_Word_Array = [0, 0, 0, 0]
errorCheckArray = [] #
for i in range (len(word_Array)):
if (int(len(D[word_Array[i]]))>= int(count_Threshold)):
word_Count = len(D[word_Array[i]])
word = word_Array[i]
for j in range (len(letter_Array)):
new_Word = str(word + str(letter_Array[j]))
try:
new_Word_Count = len(D[new_Word])
except KeyError:
new_Word_Count = 0
grown_Word_Array[j] = float(new_Word_Count) / word_Count
if (grown_Word_Array[0] <= (weighted_Prob_Array[0] + .05)) :
if (grown_Word_Array[1] <= (weighted_Prob_Array[1] + .05)) :
if (grown_Word_Array[2] <= (weighted_Prob_Array[2] + .05)) :
if (grown_Word_Array[3] <= (weighted_Prob_Array[3] + .05)) :
D2[word] = D[word]
else :
errorCheckArray.append(D[word])#
print 'hi says crake'
print len(errorCheckArray)#
## word_A = word + 'A'
##
##
##
## word_C = word + 'C'
## word_G = word + 'G'
## word_T = word + 'T'
return D2
def array_Build_B(seq_Length, Dictionary):
array_Built = [0 for a in range(seq_Length)]
word_Array = dictionaryToArrays.dictionary_To_Arrays(Dictionary)[0]
every_Word = 0
for every_Word in range(len(word_Array)):
location_Array = Dictionary[word_Array[every_Word]]
word_Length = len(word_Array[every_Word])
for every_Occurence in range(len(location_Array)):
for every_Letter in range(word_Length):
array_Built[(
location_Array[every_Occurence] + every_Letter)] += (
1 +
int(len(location_Array) * float(word_Length) / 100))
return array_Built
def letter_Look_Ahead_Alpha(D, P_of_Occur, count_Threshold) :
D2 = {}
word_Array = []
hold_Array = dictionaryToArrays.dictionary_To_Arrays(D)
word_Array = hold_Array[0]
letter_Array = ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M', 'N', 'O', 'P', 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z']
grown_Word_Array = [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]
errorCheckArray = [] #
for i in range (len(word_Array)):
if (int(len(D[word_Array[i]]))>= int(count_Threshold)):
word_Count = len(D[word_Array[i]])
word = word_Array[i]
for j in range (len(letter_Array)):
new_Word = str(word + str(letter_Array[j]))
try:
new_Word_Count = len(D[new_Word])
except KeyError:
new_Word_Count = 0
grown_Word_Array[j] = float(new_Word_Count) / word_Count
if (grown_Word_Array[0] <= P_of_Occur) :
if (grown_Word_Array[1] <= P_of_Occur) :
if (grown_Word_Array[2] <= P_of_Occur) :
if (grown_Word_Array[3] <= P_of_Occur) :
D2[word] = D[word]
else :
errorCheckArray.append(D[word])#
print 'hi says crake'
print len(errorCheckArray)#
## word_A = word + 'A'
##
##
##
## word_C = word + 'C'
## word_G = word + 'G'
## word_T = word + 'T'
return D2
def array_Build(seq_Length, Dictionary, seq):
array_Built = [0 for a in range(seq_Length)]
word_Array = dictionaryToArrays.dictionary_To_Arrays(Dictionary)[0]
every_Word = 0
for every_Word in range(len(word_Array)):
location_Array = Dictionary[word_Array[every_Word]]
word_Length = len(word_Array[every_Word])
for every_Occurence in range(len(location_Array)):
for every_Letter in range(word_Length):
if (str(seq[(location_Array[every_Occurence] + every_Letter)])
!= str("N")
): #Prevents "N" character from impacting barcode
array_Built[(location_Array[every_Occurence] +
every_Letter)] += 1
return array_Built
def threshold_Edit(D, count_Threshold, length_Threshold):
D2 = {}
word_Array = []
count_Array = []
hold_Array = []
hold_Array = dictionaryToArrays.dictionary_To_Arrays(D)
word_Array = hold_Array[0]
threshold_Word_Array = []
threshold_Count_Array = []
for i in range (len(word_Array)):
if (int(len(D[word_Array[i]])) >= int(count_Threshold)):
if (len(word_Array[i]) >= int(length_Threshold)):
#flipWord = word_Array[i]#*
#flipWord = flipWord[::-1]#*
threshold_Word_Array.append(word_Array[i])
D2[word_Array[i]] = D[word_Array[i]]
return D2