Same as #5555675. bit with static typing of the ints, for cython.
import re | |
import string | |
def main(): | |
file = open("Homo_sapiens.GRCh37.67.dna_rm.chromosome.Y.fa","r") | |
cdef int a, t, c, g | |
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") | |
cdef int totalBaseCount = a + t + c + g | |
cdef int gcCount = g + c | |
gcFraction = float(gcCount) / totalBaseCount | |
print( gcFraction * 100 ) | |
if __name__ == '__main__': | |
main() |
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