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My code, with improvents Thomas Koch, and lelledumbo.
import re
import string
def main():
file = open("Homo_sapiens.GRCh37.67.dna_rm.chromosome.Y.fa","r")
a = 0
t = 0
g = 0
c = 0
for line in file:
if not line.startswith(">"):
g += line.count("G")
c += line.count("C")
a += line.count("A")
t += line.count("T")
totalBaseCount = a + t + c + g
gcCount = g + c
gcFraction = float(gcCount) / totalBaseCount
print( gcFraction * 100 )
if __name__ == '__main__':
main()
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