source code
# The Computer Language Benchmarks Game
# https://salsa.debian.org/benchmarksgame-team/benchmarksgame/
#
# submitted by Ian Osgood
# modified by Sokolov Yura
# modified by bearophile
# 2to3
from sys import stdin
def gen_freq(seq, frame, frequences):
ns = len(seq) + 1 - frame
frequences.clear()
for ii in range(ns):
nucleo = seq[ii:ii + frame]
if nucleo in frequences:
frequences[nucleo] += 1
else:
frequences[nucleo] = 1
return ns, frequences
def sort_seq(seq, length, frequences):
n, frequences = gen_freq(seq, length, frequences)
l = sorted(list(frequences.items()), reverse=True, key=lambda seq_freq: (seq_freq[1],seq_freq[0]))
print('\n'.join("%s %.3f" % (st, 100.0*fr/n) for st,fr in l))
print()
def find_seq(seq, s, frequences):
n,t = gen_freq(seq, len(s), frequences)
print("%d\t%s" % (t.get(s, 0), s))
def main():
frequences = {}
for line in stdin:
if line[0:3] == ">TH":
break
seq = []
for line in stdin:
if line[0] in ">;":
break
seq.append( line[:-1] )
sequence = "".join(seq).upper()
for nl in 1,2:
sort_seq(sequence, nl, frequences)
for se in "GGT GGTA GGTATT GGTATTTTAATT GGTATTTTAATTTATAGT".split():
find_seq(sequence, se, frequences)
main()
notes, command-line, and program output
NOTES:
64-bit Ubuntu quad core
Python 3.12.2
Tue, 02 Apr 2024 21:17:23 GMT
MAKE:
mv knucleotide.python3 knucleotide.py
pyright .
0 errors, 0 warnings, 0 informations
4.08s to complete and log all make actions
COMMAND LINE:
/opt/src/Python-3.12.2/bin/python3 -OO knucleotide.py 0 < knucleotide-input25000000.txt
PROGRAM OUTPUT:
A 30.295
T 30.151
C 19.800
G 19.754
AA 9.177
TA 9.132
AT 9.131
TT 9.091
CA 6.002
AC 6.001
AG 5.987
GA 5.984
CT 5.971
TC 5.971
GT 5.957
TG 5.956
CC 3.917
GC 3.911
CG 3.909
GG 3.902
1471758 GGT
446535 GGTA
47336 GGTATT
893 GGTATTTTAATT
893 GGTATTTTAATTTATAGT