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Convert sequential if-statements to O(1) dictionary lookups #7

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Convert sequential if-statements to O(1) dictionary lookups #7

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119 changes: 34 additions & 85 deletions CROPSR.py
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Original file line number Diff line number Diff line change
Expand Up @@ -167,18 +167,16 @@ def rs1_score(sequence):
seq = str(sequence).upper()
seq = list(seq)
matrix1 = np.zeros([len(sequence),4], dtype=int)
baseIndex = {
'A': 0,
'T': 1,
'U': 1,
'C': 2,
'G': 3
}
for i,item in enumerate(sequence):
if item == 'A':
matrix1[i,0] = 1
if item == 'T':
matrix1[i,1] = 1
if item == 'U':
matrix1[i,1] = 1
if item == 'C':
matrix1[i,2] = 1
if item == 'G':
matrix1[i,3] = 1

index = baseIndex[item.upper()]
matrix1[i,index] = 1

"""
Generates a binary matrix for DNA/RNA sequence, where each column is a possible
Expand All @@ -192,40 +190,28 @@ def rs1_score(sequence):
basepair = sequence[i]+sequence[i+1]
pairwise_sequence.append(basepair)
matrix2 = np.zeros([len(pairwise_sequence),16], dtype=int)
for i,item in enumerate(pairwise_sequence):
if item == 'AA':
matrix2[i,0] = 1
if item == 'AT':
matrix2[i,1] = 1
if item == 'AC':
matrix2[i,2] = 1
if item == 'AG':
matrix2[i,3] = 1
if item == 'TA':
matrix2[i,4] = 1
if item == 'TT':
matrix2[i,5] = 1
if item == 'TC':
matrix2[i,6] = 1
if item == 'TG':
matrix2[i,7] = 1
if item == 'CA':
matrix2[i,8] = 1
if item == 'CT':
matrix2[i,9] = 1
if item == 'CC':
matrix2[i,10] = 1
if item == 'CG':
matrix2[i,11] = 1
if item == 'GA':
matrix2[i,12] = 1
if item == 'GT':
matrix2[i,13] = 1
if item == 'GC':
matrix2[i,14] = 1
if item == 'GG':
matrix2[i,15] = 1
pairIndex = {
'AA': 0,
'AT': 1,
'AC': 2,
'AG': 3,
'TA': 4,
'TT': 5,
'TC': 6,
'TG': 7,
'CA': 8,
'CT': 9,
'CC': 10,
'CG': 11,
'GA': 12,
'GT': 13,
'GC': 14,
'GG': 15,
}

for i,item in enumerate(pairwise_sequence):
index = pairIndex[item.upper()]
matrix2[i,index] = 1

"""
Scoring matrix
Expand Down Expand Up @@ -275,52 +261,15 @@ def rs1_score(sequence):
def posit(key):
return int(key[1:])-1
for k,v in first_order_scores.items():
if k[0] == 'A':
first_matrix[0,posit(k)] = v
elif k[0] == 'T':
first_matrix[1,posit(k)] = v
elif k[0] == 'C':
first_matrix[2,posit(k)] = v
elif k[0] == 'G':
first_matrix[3,posit(k)] = v

index = baseIndex[k[0].upper()]
first_matrix[index, posit(k)] = v

# order 2 score matrix
""" row order == AA AT AC AG TA TT TC TG CA CT CC CG GA GT GC GG """
second_matrix = np.zeros([16,29], dtype=float)
for k,v in second_order_scores.items():
if k[0:2] == 'AA':
second_matrix[0,int(k[2:])-1] = v
if k[0:2] == 'AT':
second_matrix[1,int(k[2:])-1] = v
if k[0:2] == 'AC':
second_matrix[2,int(k[2:])-1] = v
if k[0:2] == 'AG':
second_matrix[3,int(k[2:])-1] = v
if k[0:2] == 'TA':
second_matrix[4,int(k[2:])-1] = v
if k[0:2] == 'TT':
second_matrix[5,int(k[2:])-1] = v
if k[0:2] == 'TC':
second_matrix[6,int(k[2:])-1] = v
if k[0:2] == 'TG':
second_matrix[7,int(k[2:])-1] = v
if k[0:2] == 'CA':
second_matrix[8,int(k[2:])-1] = v
if k[0:2] == 'CT':
second_matrix[9,int(k[2:])-1] = v
if k[0:2] == 'CC':
second_matrix[10,int(k[2:])-1] = v
if k[0:2] == 'CG':
second_matrix[11,int(k[2:])-1] = v
if k[0:2] == 'GA':
second_matrix[12,int(k[2:])-1] = v
if k[0:2] == 'GT':
second_matrix[13,int(k[2:])-1] = v
if k[0:2] == 'GC':
second_matrix[14,int(k[2:])-1] = v
if k[0:2] == 'GG':
second_matrix[15,int(k[2:])-1] = v
index = pairIndex[k[0:2].upper()]
second_matrix[index, int(k[2:])-1] = v

item_gc = sequence[0][5:-5]
gc_count = item_gc.count('G') + item_gc.count('C')
Expand Down
142 changes: 58 additions & 84 deletions cropsr_functions.py
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,17 +12,16 @@ def one_base_matrix(sequence):
seq = str(sequence).upper()
seq = list(seq)
matrix = zeros([len(sequence),4], dtype=int)
baseIndex = {
'A': 0,
'T': 1,
'U': 1,
'C': 2,
'G': 3
}
for i,item in enumerate(sequence):
if item == 'A':
matrix[i,0] = 1
if item == 'T':
matrix[i,1] = 1
if item == 'U':
matrix[i,1] = 1
if item == 'C':
matrix[i,2] = 1
if item == 'G':
matrix[i,3] = 1
index = baseIndex[item.upper()]
matrix[i,index] = 1
return matrix


Expand All @@ -42,39 +41,27 @@ def pairwise_matrix(sequence):
basepair = sequence[i]+sequence[i+1]
pairwise_sequence.append(basepair)
matrix = zeros([len(pairwise_sequence),16], dtype=int)
pairIndex = {
'AA': 0,
'AT': 1,
'AC': 2,
'AG': 3,
'TA': 4,
'TT': 5,
'TC': 6,
'TG': 7,
'CA': 8,
'CT': 9,
'CC': 10,
'CG': 11,
'GA': 12,
'GT': 13,
'GC': 14,
'GG': 15,
}
for i,item in enumerate(pairwise_sequence):
if item == 'AA':
matrix[i,0] = 1
if item == 'AT':
matrix[i,1] = 1
if item == 'AC':
matrix[i,2] = 1
if item == 'AG':
matrix[i,3] = 1
if item == 'TA':
matrix[i,4] = 1
if item == 'TT':
matrix[i,5] = 1
if item == 'TC':
matrix[i,6] = 1
if item == 'TG':
matrix[i,7] = 1
if item == 'CA':
matrix[i,8] = 1
if item == 'CT':
matrix[i,9] = 1
if item == 'CC':
matrix[i,10] = 1
if item == 'CG':
matrix[i,11] = 1
if item == 'GA':
matrix[i,12] = 1
if item == 'GT':
matrix[i,13] = 1
if item == 'GC':
matrix[i,14] = 1
if item == 'GG':
matrix[i,15] = 1
index = pairIndex[item.upper()]
matrix[i,index] = 1
return matrix


Expand Down Expand Up @@ -126,52 +113,41 @@ def rs1_score(sequence):
# order 1 score matrix
""" row order == A T/U C G """
first_matrix = zeros([4,30], dtype=int)
baseIndex = {
'A': 0,
'T': 1,
'U': 1,
'C': 2,
'G': 3
}
for k,v in first_order_scores.items():
if k[0] == 'A':
first_matrix[0,int(k[1:])-1] = v
if k[0] == 'T':
first_matrix[1,int(k[1:])-1] = v
if k[0] == 'C':
first_matrix[2,int(k[1:])-1] = v
if k[0] == 'G':
first_matrix[3,int(k[1:])-1] = v
index = baseIndex[k[0].upper()]
first_matrix[index, int(k[1:])-1] = v

# order 2 score matrix
""" row order == AA AT AC AG TA TT TC TG CA CT CC CG GA GT GC GG """
second_matrix = zeros([16,29], dtype=int)
pairIndex = {
'AA': 0,
'AT': 1,
'AC': 2,
'AG': 3,
'TA': 4,
'TT': 5,
'TC': 6,
'TG': 7,
'CA': 8,
'CT': 9,
'CC': 10,
'CG': 11,
'GA': 12,
'GT': 13,
'GC': 14,
'GG': 15,
}
for k,v in second_order_scores.items():
if k[0:2] == 'AA':
second_matrix[0,int(k[2:])-1] = v
if k[0:2] == 'AT':
second_matrix[1,int(k[2:])-1] = v
if k[0:2] == 'AC':
second_matrix[2,int(k[2:])-1] = v
if k[0:2] == 'AG':
second_matrix[3,int(k[2:])-1] = v
if k[0:2] == 'TA':
second_matrix[4,int(k[2:])-1] = v
if k[0:2] == 'TT':
second_matrix[5,int(k[2:])-1] = v
if k[0:2] == 'TC':
second_matrix[6,int(k[2:])-1] = v
if k[0:2] == 'TG':
second_matrix[7,int(k[2:])-1] = v
if k[0:2] == 'CA':
second_matrix[8,int(k[2:])-1] = v
if k[0:2] == 'CT':
second_matrix[9,int(k[2:])-1] = v
if k[0:2] == 'CC':
second_matrix[10,int(k[2:])-1] = v
if k[0:2] == 'CG':
second_matrix[11,int(k[2:])-1] = v
if k[0:2] == 'GA':
second_matrix[12,int(k[2:])-1] = v
if k[0:2] == 'GT':
second_matrix[13,int(k[2:])-1] = v
if k[0:2] == 'GC':
second_matrix[14,int(k[2:])-1] = v
if k[0:2] == 'GG':
second_matrix[15,int(k[2:])-1] = v
index = pairIndex[k[0:2].upper()]
second_matrix[index, int(k[2:])-1] = v

item_gc = sequence[0][5:-5]
gc_count = item_gc.count('G') + item_gc.count('C')
Expand Down Expand Up @@ -321,5 +297,3 @@ def save_dataframe_to_tmp(data):
dataframe = dataframe.append(dataline,ignore_index=True)
with open(tmp_file_name, 'wb') as temp_path:
return dataframe.to_csv(temp_path)