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16-CONS.py
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16-CONS.py
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# 16) Consensus and Profile
import sys
import os
def sortInput(lines):
def isIdString(str):
if (str.startswith(">")):
return True
return False
dna_strings = []
for i in range(0, len(lines)):
if (isIdString(lines[i])):
str = ""
for j in range(i+1, len(lines)):
if (isIdString(lines[j])):
break
str += lines[j].strip()
dna_strings.append(str)
return dna_strings
def createProfileMatrix(dna_strings):
# dna_strings can be seen as a matrix of n rows x m columns
n = len(dna_strings)
m = len(dna_strings[0])
profile_matrix = {
'A': [None] * m,
'C': [None] * m,
'G': [None] * m,
'T': [None] * m,
}
for i in range(0, m):
countA = 0
countC = 0
countG = 0
countT = 0
for j in range(0, n):
if (dna_strings[j][i] == 'A'):
countA += 1
elif (dna_strings[j][i] == 'C'):
countC += 1
elif (dna_strings[j][i] == 'G'):
countG += 1
elif (dna_strings[j][i] == 'T'):
countT += 1
profile_matrix['A'][i] = countA
profile_matrix['C'][i] = countC
profile_matrix['G'][i] = countG
profile_matrix['T'][i] = countT
return profile_matrix
def createConsensusString(P):
m = len(P['A'])
consensus_string = ""
for i in range(0, m):
genomes = ['A', 'C', 'G', 'T']
counts = [P['A'][i], P['C'][i], P['G'][i], P['T'][i]]
max_index = counts.index(max(counts))
consensus_string += genomes[max_index]
return consensus_string
def main():
# Get multiline input
lines = sys.stdin.readlines()
dna_strings = sortInput(lines)
P = createProfileMatrix(dna_strings)
C = createConsensusString(P)
print(C)
for key, value in P.items():
print(str(key) + ":", *value)
if __name__ == '__main__':
if not os.environ.get("ONLINE_JUDGE"):
sys.stdin = open('./input.txt', 'r')
sys.stdout = open('./output.txt', 'w')
main()