A Python version gets a lot slower when str.count(I) is inhibited.

gc.py

#!/usr/bin/python

def main():
    gcCount = 0
    atCount = 0
    with open("Homo_sapiens.GRCh37.67.dna_rm.chromosome.Y.fa", "r") as f:
        for line in f:
            if not line.startswith('>'):
                # gcCount += line.count('G') + line.count('C')
                # atCount += line.count('A') + line.count('T')
                for c in line:
                    if c == 'G' or c == 'C':
                        gcCount += 1
                    elif c == 'A' or c == 'T':
                        atCount += 1

    print(gcCount * 100.0 / (gcCount + atCount))

if __name__ == '__main__':
    main()

# eof