Skip to content

Instantly share code, notes, and snippets.

What would you like to do?
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__':
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
You can’t perform that action at this time.