SkewArray.py

# SkewArray's point is to calculate G-C occurences (so far) for each position of the Genome
# The final purpose is to find OriC for CIRCULAR bacterial genome
# hipothesis: G - C
# positive on the forward half-strand (Ori -> term) C low G high (C mutates to T because this is a single strand longer -> okazaki fragments)
# negative on the reverse half-strand (term -> Ori) G low C high


import matplotlib.pyplot as plt


def calculateDiff(sy):
   return  -1 if sy == 'C' else 1 if sy == 'G' else 0

# Input:  A String Genome
# Output: The skew array of Genome as a list.

def SkewArray(Genome):
    skew = [0] # set zero position as zero on purpose
    for index in range(1, len(Genome) +  1):
        skew.append(skew[index - 1] + calculateDiff(Genome[index - 1]))
    return skew



# Test
# skew = SkewArray('GAGCCACCGCGATA')
# skew_dict = { i : skew[i] for i in range(len(skew))}
# print(" ".join([str(x) for x in SkewArray('GAGCCACCGCGATA')]))


# if __name__ == "__main__":
#     import sys
#     if len(sys.argv[1:]) != 1:
#         print("You must pass a genome string argument")
#         exit()
#     with open(sys.argv[1],'r') as file:
#         genome = file.read()

#         skew = SkewArray(genome)
#         plt.plot(skew)
#         plt.xlabel('Genome position')
#         plt.ylabel('skew (difference G - C)')
#         plt.show()