/Peculiar-Statistics-of-the-Forward-and-Reverse-Half-Strands

Python applications to Genomics

Input: Strings Genome and symbol

symbol = "A" Genome = "AAAAGGGG"

Output: SymbolArray(Genome, symbol)

def SymbolArray(Genome, symbol): array = {} n = len(Genome) ExtendedGenome = Genome + Genome[0:n//2] for i in range(n): array[i] = PatternCount(symbol, ExtendedGenome[i:i+(n//2)]) return array

Reproduce the PatternCount function here

def PatternCount(symbol,ExtendedGenome): count = 0 for i in range(0,len(ExtendedGenome)-len(symbol)+1): if ExtendedGenome[i:i+len(symbol)] == symbol: count = count+1 return count

Input: Strings Genome and symbol

Genome = "AAAAGGGG" symbol = "A"

Output: FasterSymbolArray(Genome, symbol)

def FasterSymbolArray(Genome, symbol): array = {} n= len(Genome) ExtendedGenome = Genome + Genome[0:n//2]

#look at the first half of Genome to compute first array value
array[0] = PatternCount(symbol, Genome[0:n//2])

for i in range(1, n):
    #start by setting the current array value equal to the previous array value
    array[i] = array[i - 1]
    
    #the current array value can differ from the previous a value by at most 1
    if ExtendedGenome[i - 1] == symbol:
        array[i] = array[i] - 1
    if ExtendedGenome[i + (n//2) - 1] == symbol:
        array[i] = array[i] + 1
return array

Output: The number of times Pattern appears in Text

def PatternCount(symbol, Genome): count = 0 # output variable k = len(symbol) n = len(Genome) for i in range(n - k + 1): if symbol[i:i+k] == Genome: count += 1 return Genome.count(symbol)

import sys lines = sys.stdin.read().splitlines() print(FasterSymbolArray(lines[0],lines[1]))