performance measurements
Each table row shows performance measurements for this Python 3 program with a particular command-line input value N.
| N | CPU secs | Elapsed secs | Memory KB | Code B | ≈ CPU Load |
|---|---|---|---|---|---|
| 1,000 | 0.02 | 0.02 | ? | 878 | 0% 0% 67% 33% 0% 0% 0% 0% |
Read the ↓ make, command line, and program output logs to see how this program was run.
Read reverse-complement benchmark to see what this program should do.
notes
Python 3.3.1 (default, Apr 11 2013, 12:45:45) [GCC 4.7.2] on linux
reverse-complement Python 3 #6 program source code
# The Computer Language Benchmarks Game
# http://benchmarksgame.alioth.debian.org/
#
# contributed by Joerg Baumann
from sys import stdin, stdout
from os import cpu_count
reverse_translation = bytes.maketrans(
b'ABCDGHKMNRSTUVWYabcdghkmnrstuvwy',
b'TVGHCDMKNYSAABWRTVGHCDMKNYSAABWR')
def reverse_complement(header, sequence):
t = sequence.translate(reverse_translation, b'\n\r ')
output = bytearray()
trailing_length = len(t) % 60
if trailing_length: output += b'\n' + t[:trailing_length]
for i in range(trailing_length, len(t), 60):
output += b'\n'+ t[i:i+60]
return header, output[::-1]
def read_sequences(file):
for line in file:
if line[0] == ord('>'):
header = line
sequence = bytearray()
for line in file:
if line[0] == ord('>'):
yield header, sequence
header = line
sequence = bytearray()
else:
sequence += line
yield header, sequence
break
def reverse_and_print_task(q, c, v):
while True:
i = q.get()
if i == None: break
h, r = reverse_complement(*data[i])
with c:
while i != v.value:
c.wait()
write(h); write(r); flush()
with c:
v.value = i + 1
c.notify_all()
if __name__=='__main__' :
write = stdout.buffer.write
flush = stdout.buffer.flush
s = read_sequences(stdin.buffer)
data = next(s)
if cpu_count() == 1 or len(data[1]) < 1000000:
from itertools import starmap
def merge(v, g):
yield v; yield from g
for h, r in starmap(reverse_complement, merge(data, s)):
write(h); write(r)
else:
from multiprocessing import Process, Queue, Value, Condition
from ctypes import c_int
data = [data] + list(s)
q, c, v = (Queue(), Condition(), Value(c_int, 0))
processes = [Process(target=reverse_and_print_task, args=(q, c, v))
for _ in range(min(len(data), cpu_count()))]
for p in processes: p.start()
for i in range(len(data)): q.put(i)
for p in processes: q.put(None)
for p in processes: p.join()
make, command-line, and program output logs
Sun, 30 Jul 2023 10:53:14 GMT COMMAND LINE: /usr/bin/python3 revcomp.python3-6.python3 0 < revcomp-input1000.txt (TRUNCATED) PROGRAM OUTPUT: >ONE Homo sapiens alu CGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAC CTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACA GGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCAT GTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAA AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCTTTTTGAGACGGAGTCTCGCTC TGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGG GTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACC ACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTG GTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTA CAGGCGTGAGCCACCGCGCCCGGCCTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCT GGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTC TCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGGCTAAT TTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCT GACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCA CCGCGCCCGGCCTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGC GCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCC TCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTTA GTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGAT CCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCT TTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTC ACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTG GGATTACAGGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGT TTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGG CCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCTTTTTGAGACGGAG TCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCG CCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGC GCGCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGG CCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGC TGGGATTACAGGCGTGAGCCACCGCGCCCGGCCTTTTTGAGACGGAGTCTCGCTCTGTCG CCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCA AGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCC CGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTC GAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGC GTGAGCCACCGCGCCCGGCC >TWO IUB ambiguity codes TAGGDHACHATCRGTRGVTGAGWTATGYTGCTGTCABACDWVTRTAAGAVVAGATTTNDA GASMTCTGCATBYTTCAAKTTACMTATTACTTCATARGGYACMRTGTTTTYTATACVAAT TTCTAKGDACKADACTATATNTANTCGTTCACGBCGYSCBHTANGGTGATCGTAAAGTAA CTATBAAAAGATSTGWATBCSGAKHTTABBAACGTSYCATGCAAVATKTSKTASCGGAAT WVATTTNTCCTTCTTCTTDDAGTGGTTGGATACVGTTAYMTMTBTACTTTHAGCTAGBAA AAGAGKAAGTTRATWATCAGATTMDDTTTAAAVAAATATTKTCYTAAATTVCNKTTRACG ADTATATTTATGATSADSCAATAWAGCGRTAGTGTAAGTGACVGRADYGTGCTACHVSDT CTVCARCSYTTAATATARAAAATTTAATTTACDAATTGBACAGTAYAABATBTGCAGBVG TGATGGDCAAAATBNMSTTABKATTGGSTCCTAGBTTACTTGTTTAGTTTATHCGATSTA AAGTCGAKAAASTGTTTTAWAKCAGATATACTTTTMTTTTGBATAGAGGAGCMATGATRA AAGGNCAYDCCDDGAAAGTHGBTAATCKYTBTACBGTBCTTTTTGDTAASSWTAAWAARA TTGGCTAAGWGRADTYACATAGCTCBTAGATAWAGCAATNGTATMATGTTKMMAGTAWTC CCNTSGAAWATWCAAAAMACTGAADNTYGATNAATCCGAYWNCTAACGTTAGAGDTTTTC ATCTGGKRTAVGAABVCTGWGBTCTDVGKATTBTCTAAGGVADAAAVWTCTAGGGGAGGG TTAGAACAATTAAHTAATNAAATGCATKATCTAAYRTDTCAGSAYTTYHGATRTTWAVTA BGNTCDACAGBCCRCAGWCRTCABTGMMAWGMCTCAACCGATRTGBCAVAATCGTDWDAA CAYAWAATWCTGGTAHCCCTAAGATAACSCTTAGTGSAACAWTBGTCDTTDGACWDBAAC HTTTNGSKTYYAAYGGATNTGATTTAARTTAMBAATCTAAGTBTCATYTAACTTADTGTT TCGATACGAAHGGCYATATACCWDTKYATDCSHTDTCAAAATGTGBACTGSCCVGATGTA TCMMAGCCTTDAAABAATGAAGAGTAACTHATMGVTTAATAACCCGGTTVSANTGCAATT GTGAGATTTAMGTTTAMAAYGCTGACAYAAAAAGGCACAMYTAAGVGGCTGGAABVTACG GATTSTYGTBVAKTATWACCGTGTKAGTDTGTATGTTTAAAGGAAAAAGTAACATARAAA GGTYCAMNYAAABTATAGNTSATANAGTCATCCTATWADKAACTRGTMSACDGTATSAYT AAHSHGTAABYGACTYTATADTGSTATAGAGAAATCGNTAAAGGAAATCAGTTGTNCYMV TNACDRTATBNATATASTAGAAMSCGGGANRCKKMCAAACATTNAGTCTRMAATBMTACC CGTACTTCTBGDSYAATWGAAAATGACADDCHAKAAAYATATTKTTTTCACANACWAGAA AKATCCTTATTAYKHKCTAAACARTATTTTDATBTVWCYGCAATACTAGGKAAASTTDGA MGGCHTTHAATVCAHDRYAGGRCTATACGTCMAGAGAGCTBTHGNACARTCCBDCTAAGA GCGGCTTTARTAAAGAATCCNAGTAWBTGACTTGAATTACWTVACAGAAABCAATNAAAC CGTNTRANTTGAYCMAWBADTANABRGGTKTHTWTAGTTVCTMBKTAGMTVKCCAGCANT TVAGSWTTAGCCGCRHTTTCCTTHNTATTAAGAAGAATAGGMTRAARTCTABGTACDTTT TATAAVDHAHTATAGATCCTAGTAAGYTWATDWCATGAGGGATAGTAAMDMNGBASTWAM TSTATRBAYDABATGTATATYCGCACTGTTTTAACMCWBTATAWAGTATBTSTATVTTAR CCTMTTAAKADATCAACTAATYTSVTAKGDATTATGCKTCAYCAKAATACTTKAANGAGT ATTSDAGATCGGAAATACTTAAYAAVGTATMCGCTTGTGTDCTAATYTATTTTATTTWAA CAGWRCTATGTAGMTGTTTGTTYKTNGTTKTCAGAACNTRACCTACKTGSRATGTGGGGG CTGTCATTAAGTAAATNGSTTABCCCCTCGCAGCTCWHTCGCGAAGCAVATGCKACGHCA ACAKTTAATAACASAAADATTWNYTGTAATTGTTCGTMHACHTWATGTGCWTTTTGAAHY ACTTTGTAYAMSAAACTTAADAAATATAGTABMATATYAATGSGGTAGTTTGTGTBYGGT TWSGSVGWMATTDMTCCWWCABTCSVACAGBAATGTTKATBGTCAATAATCTTCTTAAAC ARVAATHAGYBWCTRWCABGTWWAATCTAAGTCASTAAAKTAAGVKBAATTBGABACGTA AGGTTAAATAAAAACTRMDTWBCTTTTTAATAAAAGATMGCCTACKAKNTBAGYRASTGT ASSTCGTHCGAAKTTATTATATTYTTTGTAGAACATGTCAAAACTWTWTHGKTCCYAATA AAGTGGAYTMCYTAARCSTAAATWAKTGAATTTRAGTCTSSATACGACWAKAASATDAAA TGYYACTSAACAAHAKTSHYARGASTATTATTHAGGYGGASTTTBGAKGATSANAACACD TRGSTTRAAAAAAAACAAGARTCVTAGTAAGATAWATGVHAAKATWGAAAAGTYAHVTAC TCTGRTGTCAWGATRVAAKTCGCAAVCGASWGGTTRTCSAMCCTAACASGWKKAWDAATG ACRCBACTATGTGTCTTCAAAHGSCTATATTTCGTVWAGAAGTAYCKGARAKSGKAGTAN TTTCYACATWATGTCTAAAADMDTWCAATSTKDACAMAADADBSAAATAGGCTHAHAGTA CGACVGAATTATAAAGAHCCVAYHGHTTTACATSTTTATGNCCMTAGCATATGATAVAAG >THREE Homo sapiens frequency ATATTTATCTTTTCACTTCCTACATTGGTCAGACCATTATTCGACACGTGGCGTCATTTT GTCATACCGGGTAATGTTGGAAACAAAACGTACTGATAAAATACTGAGTTGTAAACTCTA ATCAGATAACGCGCTTGGATATTAAGATTCACACAGGGGTTTCGGCTGTAAAAAAACTTG TGGAGCTGTTCTGGGACAGATAAGTTGTACCTCGTACTTAGCTAATTAATGAACCAACTG ATTACGATAGAACAATTCTGAGGCCGCCAGGACAGCCAAATTTTAATCTTATAAAGCTGG AAACAGCCGGTATTAGCTTCTCGCATACTTTGCCTGCATTGGTACCTTACAGATATCAGC GTAGTCATATACACCTCGGTCTCAGCTAAGCTTGTATCTCTTAGAGTAGTTCAAAGATAG TGGACAATACCTGTGGAATCGATTGCAGATATGGATTTATTTAACTACTGAGTCTCATTC ACAAGCTAAGCAAGGAGCACGTTTTGGTGCCGGCATACCGATTTGCTATCATGTCAGCAA ATTTGCGTTGTATTCCTAGTTGCACCCATTAAGGCCACACTCCGAACCTAATTATTACAT CGCAAAGACATGTACGAAGGACCCGATGTCGAATAGAAGGGAGGACTGTTCATTGGAAGC TAGACCAGAGGAATCGCAAAGATGCAACTCTTACAATAAAAATCTAATTTCAGTCAACAC GCAATTTCTATAAGGTTTCCGATAATAATGAACCGTCTTCCACAGGGGAATTTGCCATGC TCGTAAAAGTAGTTAATCCAAGTAGAAGAAATTTTGATAATGTTTTAAGTTGGCACGAAG GAATTCAGAGAGATCTTACCTAACAAAGGCATTAGTAGATGTTCCTTGGTTCACACTCGG TCAATCAGAGCACATACTACGGGCGATACCGGGAATGACACAACATCAATGAGATTGTTA AGTGAGGTAATTGACTTTAGAGGACTCGATCAGTATACTGTCACTATGAACATCGTATTA ATTGTTATCCGATATATACACCACCGATTTGCTTGTGCAAGGTTACAGACCCATTCGATA AATACAAACACGGAGCGATATTATTTAAGGAGTGCTGTCTTCAAAAGAATTATTCCCACA CCGACATAAGAACTTCGCTCCGTCATTCCAGATTTAAATAACATAACGTAACGCTTTGCT GATAACATAACATAACCGAGAATTTGCTTAGGAAATTTGGAGCAATATTGCATTGTTTCT CAGTCATCACAAGGCCCGCCAAAGAACTCTGAGAATCAGGATTCAACATGATTGGTAAGA CTCTATATATATAACTTAATTCTTGTGTCCGGAGATAGAAAGAGGACGAGAGATACTACG AAAGAAAGTGTACTTCGATGTATCAATTCAGACGCCTTCTCTATCATCAACATTATAGGT CTCGTATATGCTCGGCGCGATCTGCTTCTCTCCGCCAATAGCCCCATAGTGTATTTCAAG CGCAGTAACAGTGAAATCGTTACGAAGGTAGGGATGTTGCTTATAATTGTCGTAACTTAT CGCTTATGTATCTTTCAAGAATGAACGGCAGCATATACATACGTTCTACCTTTAGCTACA AAGCATCCATATACTCCCTCTCATGATTGAAACTCTTCCCTATTTTGTAGCCAATAGTGA AAGCGTATTAGTATAAATTCGTCGGTTTTTCACTCGCAACTGTTATACTCTGCAAACAAA CGAAAGCCTCATAGTACAAACCTAAAGCTACATACTTCATCATTGGCAGACCAGTGGCGG TATTTCTACGGAAGCATCACTATAGATATAAAGTTTCCCTTCATGTACGTCTGTTAACCA TATCACAAGAAACTGCTATCTCTGTCACGTAACAATTCACGCGCCTTATCGCCAAATGTT CATATATGCGCGGTATACGTATGAACGAATACTAATTAGTATAACGGAGGATTCACGGGA GGGATACTTGGGGCATTTATAAATCGTCTAAAAATTTTCTATCAGCACTTGCGGGTTATA GTGGATTACTAGGCAACATAATATTCTGTATTGGTCCAAATGACGCTATAGATAAATTAG CAAAATACATTGTTTCCATTTATGTAAGTCGAAACTCCAGGACTCCCGGGAACCAGTTAA ACCGTCTGGAAAAGACACATTGTGAGCGGGACTTCAATGATAGCTTTCAATGAGCTTCTC ATGCTTGGGGTCTGTACATATATGTTGGCGAAATTATCGTCTGTATTCTGTTATGCTTTG ATCATGGGTTATTAGTATAGTGTCCGGTTAAGTACCAATACCGCTAGAGACCCGACCTAA GTCGATAACTAACGATCATCGACGTAAGGATCGTCTCGATCAGTACTTCAGTCTAGATCT GGGAATAGTAACTCGTTAGTGAACTATGTCGTGTCATAACTCTAAAATGCAATCAAATCT TATTATTGAGTATTGATTATATAAAGCATCCGCTTAGCTTTACCCTCAAATGTTATATGC AATTTAAAGCGCTTGATATCGTCTACTCAAGTTCAGGTTTCACATGGCCGCAACGTGACG TTATTAGAGGTGGGTCATCATCTCTGAGGCTAGTGATGTTGAATACTCATTGAATGGGAA GTGGAATACCATGCTCGTAGGTAACAGCATGACCTATAAAATATACTATGGGTGTGTGGT AGATCAATATTGTTCAAGCATATCGTAACAATAACGGCTGAAATGTTACTGACATGAAAG AGGGAGTCCAAACCATTCTAACAGCTGATCAAGTCGTCTAAAAACGCCTGGTTCAGCCTT AAGAGTTATAAGCCAGACAAATTGTATCAATAGAGAATCCGTAAATTCCTCGGCCAACCT CTTGCAAAGACATCACTATCAATATACTACCGTGATCTTAATTAGTGAACTTATATAAAT ATCTACAACCAGATTCAACGGAAAAGCTTTAGTGGATTAGAAATTGCCAAGAATCACATT CATGTGGGTTCGAATGCTTTAGTAATACCATTTCGCCGAGTAGTCACTTCGCTGAACTGT CGTAAATTGCTATGACATAATCGAAAAGGATTGTCAAGAGTCGATTACTGCGGACTAATA ATCCCCACGGGGGTGGTCTCATGTCTCCCCAGGCGAGTGGGGACGGTTGATAAACACGCT GCATCGCGGACTGATGTTCCCAGTATTACATAGTCACATTGGATTGCGAGTAGTCTACCT ATTTATGAGCGAGAGATGCCTCTAACTACTTCGACTTTTAAAACCTTTCCACGCCAGTAT TCGGCGAAAGGGAAGTATTAAGGGTTGTCATAATTAAGCTGATACCACTTCAGACTTTGC TCTACTTCTGTCTTTCATTGGTTTAGTAAAGTCTGTCCATTCGTCGAGACCGTCTTTTGC AGCCTCATTCTACCAACTGCTCCGACTCTTAGTCTGCTTCTCCCAGCGTTATAACAAGAG GCATTTTGTCATCCTTAAAACAATAATAAAGAACTCGGAGCACTGATATAATGACTGAAT TAGAACCGCTTAAAAATACAACGAATAGATAAGACTATCGGATAAGATCTAATATGTAGT GATTAAGCCCTTTATTAATTAATAATAGTTACCCTTTCTGATGTAACGCGACATATTACG ATTTAGTGGCACGTCTGAATTGCAAAGCAGATCTCTACCCGATTTTTATTATAAATCCCG TATACATCTTGACTTGAGTAATTGTTCATCTTTTTATATCTCTTCGTACTACAAATAATT AATATCTCAACCCGTATTGTGTGATTCTAATTACCAACAGAATACGAGGAGGTTTTTGCT TAGGGCCATATATAATGAATCTATCTCGTTTATTCGCGGAACCCGAGATAACATTACGAT GTAACTATTTTAGAGAACTTAATACAAGAAACATTGCTGATTACTCATAACTAAATGCTT GGTAATATATCCTCAGTGCCCCTACCATCTTTTACGCAGGGATGTAATTACTTAGGATTC ATTGTGTAAGAATTACAATGAACGATGGATATGAAGGCATGTTGCGAGGTGTTCCTTGGT ATGTGAAGTTCGCAGGGCAACAAAAATTTCGCAGAATAGGCCTCAAAGTATTGGTAAAGA AGACAACTAATCATCACGAGCTTCTGATATCAATACGAACGAGTCCTGTGATGGATGAAA GAAAGTCGTATCGAAAATGTCAAGAGTCTGCCCAATGTAACTTACTTCAAAAAATAACGC TTCCGCCAAGTACGTTCGAATAAACGTAATTTTAAAAATACATAAGGGGTGTTAGAAAGT AAGCGACGGGATATAAGTTAGACTCAAGATTCCGCCGTAAAACGAGACTGATTCCGAAGA TTGTTCGTGGATCTGGTCATGACTTTCACTGAGTAAGGAGTTTCGACATATGTCAATAAA CACAAAAATAGAAGCTATTCGATCTGAAAAATATTAGGACAAGAAACTATCTCACGCTAG CCCAGAATATTCACTCACCCACGGGCGATACTAAAGCACTATATAGTCGCGTGATTACTA TACATATGGTACACATAAGAATCACGATCAGGTTCTCAATTTTCAACAATATATGTTTAT TTGCATAGGTAATATTAGGCCTTTAAGAGAAGGATGGGTGAGATACTCCGGGGATGGCGG CAATAAAGAAAAACACGATATGAGTAATAGGATCCTAATATCTTGGCGAGAGACTTAAGG TACGAATTTTGCGCAATCTATTTTTTACTTGGCCAGAATTCATGTATGGTATAAGTACGA ACTTTTTTGATCACTTTCATGGCTACCTGATTAGGATAGTTTGAGGAATTTCCCAAATAT ACCGATTTAATATACACTAGGGCTTGTCACTTTGAGTCAGAAAAAGAATATAATTACTTA GGGTAATGCTGCATACATATTCTTATATTGCAAAGGTTCTCTGGGTAATCTTGAGCCTTC ACGATACCTGGTGAAG