哪种情况会受益于Perl的研究？

Question

我正在玩研究,一个Perl功能来检查一个字符串,使后续的正则表达式可能更加快速:

while( <> ) {
    study;
    $count++ if /PATTERN/;
    $count++ if /OTHER/;
    $count++ if /PATTERN2/;
    }

关于哪些情况会从中受益的说法不多.你可以从文档中挑出一些东西:

• 具有常量字符串的模式
• 多种模式
• 较短的目标字符串可能更好(花费更少的时间来学习)

我正在寻找具体的案例,我不仅可以展示一个巨大的优势,而且还有一些案例,我可以略微调整以失去这种优势.文档中的警告之一是您应该对个别案例进行基准测试.我想找到一些边缘情况,其中字符串(或模式)中的小差异会对性能产生很大影响.

如果你还没有用过学习,请不要回答.我宁愿有完善的正确答案而不是快速猜测.这里没有紧迫感,这并没有阻碍任何工作.

而且,作为奖励,我一直在玩一个比较两个NYTProf运行的基准测试工具,我宁愿使用它而不是通常的基准测试工具.如果我想出一种自动化的方法,我也会分享.

Answer 1

谷歌出现了这个可爱的测试场景:

#!/usr/bin/perl
# 
#  Exercise 7.8 
# 
# This is a more difficult exercise. The study function in Perl may speed up searches 
# for motifs in DNA or protein. Read the Perl documentation on this function. Its use 
# is simple: given some sequence data in a variable $sequence, type:
# 
# study $sequence;
# 
# before doing the searches. Do you think study will speed up searches in DNA or 
# protein, based on what you've read about it in the documentation?
# 
# For lots of extra credit! Now read the Perl documentation on the standard module 
# Benchmark. (Type perldoc Benchmark, or visit the Perl home page at http://www.
# perl.com.) See if your guess is right by writing a program that benchmarks motif 
# searches of DNA and of protein, with and without study.
#
# Answer to Exercise 7.8

use strict;
use warnings;

use Benchmark;

my $dna = join ('', qw(
agatggcggcgctgaggggtcttgggggctctaggccggccacctactgg
tttgcagcggagacgacgcatggggcctgcgcaataggagtacgctgcct
gggaggcgtgactagaagcggaagtagttgtgggcgcctttgcaaccgcc
tgggacgccgccgagtggtctgtgcaggttcgcgggtcgctggcgggggt
cgtgagggagtgcgccgggagcggagatatggagggagatggttcagacc
cagagcctccagatgccggggaggacagcaagtccgagaatggggagaat
gcgcccatctactgcatctgccgcaaaccggacatcaactgcttcatgat
cgggtgtgacaactgcaatgagtggttccatggggactgcatccggatca
ctgagaagatggccaaggccatccgggagtggtactgtcgggagtgcaga
gagaaagaccccaagctagagattcgctatcggcacaagaagtcacggga
gcgggatggcaatgagcgggacagcagtgagccccgggatgagggtggag
ggcgcaagaggcctgtccctgatccagacctgcagcgccgggcagggtca
gggacaggggttggggccatgcttgctcggggctctgcttcgccccacaa
atcctctccgcagcccttggtggccacacccagccagcatcaccagcagc
agcagcagcagatcaaacggtcagcccgcatgtgtggtgagtgtgaggca
tgtcggcgcactgaggactgtggtcactgtgatttctgtcgggacatgaa
gaagttcgggggccccaacaagatccggcagaagtgccggctgcgccagt
gccagctgcgggcccgggaatcgtacaagtacttcccttcctcgctctca
ccagtgacgccctcagagtccctgccaaggccccgccggccactgcccac
ccaacagcagccacagccatcacagaagttagggcgcatccgtgaagatg
agggggcagtggcgtcatcaacagtcaaggagcctcctgaggctacagcc
acacctgagccactctcagatgaggaccta
));

my $protein = join('', qw(
MNIDDKLEGLFLKCGGIDEMQSSRTMVVMGGVSGQSTVSGELQD
SVLQDRSMPHQEILAADEVLQESEMRQQDMISHDELMVHEETVKNDEEQMETHERLPQ
GLQYALNVPISVKQEITFTDVSEQLMRDKKQIR
));

my $count = 1000;

print "DNA pattern matches without 'study' function:\n";
timethis($count,
    ' for(my $i=1 ; $i < 10000; ++$i) {
        $dna =~ /aggtc/;
        $dna =~ /aatggccgt/;
        $dna =~ /gatcgatcagctagcat/;
        $dna =~ /gtatgaac/;
        $dna =~ /[ac][cg][gt][ta]/;
        $dna =~ /ccccccccc/;
    } '
);

print "\nDNA pattern matches with 'study' function:\n";
timethis($count,
    ' study $dna;
    for(my $i=1 ; $i < 10000; ++$i) {
        $dna =~ /aggtc/;
        $dna =~ /aatggccgt/;
        $dna =~ /gatcgatcagctagcat/;
        $dna =~ /gtatgaac/;
        $dna =~ /[ac][cg][gt][ta]/;
        $dna =~ /ccccccccc/;
    } '
);

print "\nProtein pattern matches without 'study' function:\n";
timethis($count,
    ' for(my $i=1 ; $i < 10000; ++$i) {
        $protein =~ /PH.EI/;
        $protein =~ /KFTEQGESMRLY/;
        $protein =~ /[YAL][NVP][ISV][KQE]/;
        $protein =~ /DKKQIR/;
        $protein =~ /[MD][VT][HQ][ER]/;
        $protein =~ /NVPISVKQEITFTDVSEQL/;
    } '
);

print "\nProtein pattern matches with 'study' function:\n";
timethis($count,
    ' study $protein;
    for(my $i=1 ; $i < 10000; ++$i) {
        $protein =~ /PH.EI/;
        $protein =~ /KFTEQGESMRLY/;
        $protein =~ /[YAL][NVP][ISV][KQE]/;
        $protein =~ /DKKQIR/;
        $protein =~ /[MD][VT][HQ][ER]/;
        $protein =~ /NVPISVKQEITFTDVSEQL/;
    } '
);

请注意,对于最有利可图的案例(蛋白质匹配),报告的收益仅为约2%:

#  $ perl exer07.08
# On my computer, this is the output I get: your results probably vary.

#  DNA pattern matches without 'study' function:
#  timethis 1000: 29 wallclock secs (29.25 usr +  0.00 sys = 29.25 CPU) @ 34.19/s (n=1000)
#  
#  DNA pattern matches with 'study' function:
#  timethis 1000: 30 wallclock secs (29.21 usr +  0.15 sys = 29.36 CPU) @ 34.06/s (n=1000)
#  
#  Protein pattern matches without 'study' function:
#  timethis 1000: 32 wallclock secs (29.47 usr +  0.04 sys = 29.51 CPU) @ 33.89/s (n=1000)
#  
#  Protein pattern matches with 'study' function:
#  timethis 1000: 30 wallclock secs (28.97 usr +  0.02 sys = 28.99 CPU) @ 34.49/s (n=1000)
#