This is reasonably idiomatic Python and 10x faster than the implementation in the original post: with open("orthocoronavirinae.fasta") as f: text = ''.join((line.rstrip() for line in f.readlines() if not line.startswith('>'))) gc = text.count('G') + text.count('C') total = len(text) Or if you want to be explicit, this is just as fast (and might scale better for particularly long genomes): gc = 0 total = 0 with open("…
One liner to count gc, without buffering. import io f = io.StringIO( """ AB CD EF GH """ ) total = sum(map(lambda s: 0 if s[0]==">" else s.count('G') + s.count('C'), f.readlines())) print(total)
And reading the file as binary. There's a lesson about the overhead of unicode strings here ;)
Your first example takes 3.1 seconds, my previous comment takes 2.3 seconds, this one takes 1.4 seconds.
start = time.perf_counter()
with open("orthocoronavirinae.fasta", "rb") as f:
total = sum(map(lambda s: 0 if s[0]==65 else s.count(b"G") + s.count(b"C"), f.readlines()))
end = time.perf_counter()
print(total, " total")
print(end-start, " seconds")