Each table row shows performance measurements for this Python 2 program with a particular command-line input value N.
N | CPU secs | Elapsed secs | Memory KB | Code B | ≈ CPU Load |
---|---|---|---|---|---|
10,000 | 0.07 | 0.07 | ? | 593 | 100% 0% 0% 0% 0% 0% 0% 0% |
Read the ↓ make, command line, and program output logs to see how this program was run.
Read k-nucleotide benchmark to see what this program should do.
# The Computer Language Benchmarks Game # http://benchmarksgame.alioth.debian.org/ # # 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()
Fri, 30 Oct 2020 19:33:01 GMT COMMAND LINE: /usr/bin/python2 knucleotide.python 0 < knucleotide-input10000.txt PROGRAM OUTPUT: A 30.284 T 29.796 C 20.312 G 19.608 AA 9.212 AT 8.950 TT 8.948 TA 8.936 CA 6.166 CT 6.100 AC 6.086 TC 6.042 AG 6.036 GA 5.968 TG 5.868 GT 5.798 CC 4.140 GC 4.044 CG 3.906 GG 3.798 562 GGT 152 GGTA 15 GGTATT 0 GGTATTTTAATT 0 GGTATTTTAATTTATAGT