改进下程序

zhagnqiang829

要求：算出一个基因组序列（大约有3G）8联体的个数。
8联体是指8个由ACGT四个字母组成的序列对，共有4的8次方个（65536）。
目的：求出每个8联体出现的次数。
比如下面序列：从最开始1~8,2~9,3~10，4~11.....8个8个走，求出每个8联体出现的个数
gtatagaaatcatcgatttttcaggaaaagcaagaaagatcggtttaaaaaattatgaaattttattttaaaaatcgaaaaatcaacaaaaaaaatcgaaattttagaatttttctaaaatcggtagttttcgaaataaaataaaaatgttattttaaaaattattttaaaaaatttcgagaaattcaaaaatcgaacagaaatgttcgattttttgctacagtgcattttttttccacttctacgactttaaaggggggcgcatttatgcggaagggtcttgccgtgcacatagtcatcatttttaacaaagtctgctcaaaattcgcggagatcacgcgtagatcacaattaatttgtgaaaaagcaacagaaatacgaaatatgggataaatattttgtgatcttcatgtgatctacgcgaattttacacagaaactgctaaaaatgatgactaaatgcgcggcaagacccttccgcataaatgctcccccctttaaagtcgtagaagtaggaaaaaatgcactgtatggtgaatttgaaaattttctaaaaatccgaataatttagtatattggggtttcgacgaaaaatgccaatttttcagtaatttctggtcttttctaaaaaaatctacatatttcagatctcttcctccttttccgagttttttcgttattttttctaaactcacagtatattagcgaattttcaacaaattcgacaaaaaattctgactgttttctagaaaaaaaaaaaggcggcatgcgcaagtttcaaaatttgccgcacacctctgggcattaccttgaaagtatcaatggaaaagtgtcgcaagatttaattttctgatattccccccccccctcccgttttacttgtttctaggtttgagtttacttaaattaataacaaaactgggagatatatgctcgaaaattagacagaatctctgcctggacgatttctaggctacgccgtcattcccatagttttcataatctttcggctcagtgatcgaa
输出结果类似：
aaaaaaaa        9349.000000       
aaaaaaag        2045.000000       
aaaaaaac         2411.000000       
aaaaaaat         4831.000000       
aaaaaaga        1469.000000       
aaaaaagg        763.000000       
aaaaaagc        585.000000       
aaaaaagt         1714.000000       
aaaaaaca         1704.000000       
aaaaaacg        800.000000       
aaaaaacc         843.000000       
aaaaaact         1386.000000       
aaaaaata         2453.000000       
aaaaaatg         1972.000000       
aaaaaatc         2165.000000       
aaaaaatt         4936.000000       
aaaaagaa        1383.000000       
aaaaagag        653.000000       
aaaaagac        347.000000       

zhagnqiang829

这是我的C++程序，运行了一个星期了，还没运行完。
哪位大神帮我优化下程序。perl程序也可以，谢谢。
#include<stdio.h>
#include<stdlib.h>
#include<string.h>
#include<math.h>

#define N 65536

struct motif
{
  char name[20];
  float  number;
} lead[N];

void main()
{

        FILE *in,*out;
        in=fopen("result.txt","r");
        out=fopen("结果.txt","w");
    static char s[86000000];
        char c[4]={'a','g','c','t'};
        int i=0,j=0,k=0,l=0,m=0,n=0,p=0,q=0,r=0,number=0;
        int person=0;
        float words=0;
        float expect=0;
       
        for(i=0;i<4;i++)
         for(j=0;j<4;j++)
          for(l=0;l<4;l++)
           for(m=0;m<4;m++)
            for(n=0;n<4;n++)
             for(p=0;p<4;p++)
              for(q=0;q<4;q++)
               for(r=0;r<4;r++)
                   {
                lead[number].name[0]=c[i];
                lead[number].name[1]=c[j];
                lead[number].name[2]=c[l];
                lead[number].name[3]=c[m];
                lead[number].name[4]=c[n];
                lead[number].name[5]=c[p];
                lead[number].name[6]=c[q];
                lead[number].name[7]=c[r];
                number++;
                   }

    while(!feof(in))
        {
      fgets(s,86000000,in);
          if(s[0]=='@') break;
          for(i=0;i<85999999;i++)
          {
           for(j=0;j<4;j++)
                for(k=0;k<4;k++)
                 for(l=0;l<4;l++)
                  for(m=0;m<4;m++)
                   for(n=0;n<4;n++)
                    for(p=0;p<4;p++)
                     for(q=0;q<4;q++)
                      for(r=0;r<4;r++)
                          {
                       if(s[i]==c[j]&&s[i+1]==c[k]&&s[i+2]==c[l]&&s[i+3]==c[m]&&s[i+4]==c[n]&&s[i+5]==c[p]&&s[i+6]==c[q]&&s[i+7]==c[r])
                                  lead[person].number++;
               person++;
                          }  
       person=0;
       words++;
          }
           
          for(i=0;i<85999999;i++)
                s[i]=' ';
           }

    fprintf(out,"The Number of total words are %f\n",words);

    expect=words/N;

    fprintf(out,"The Expect Number words are %f\n",expect);


        for(k=0;k<N;k++)               
                fprintf(out,"%s\t%f\t%f\n",lead[k].name,lead[k].number,lead[k].number/65536.0);
       
        fclose(out);
}

rubyish

1. #!perl6
   
2. my %h;
   
3. my $s = 'gtatagaaatcatcgatttttcaggaaaagcaagaaagatcggtttaaaaaattatgaaattttattttaaaaatcgaaaaatcaacaaaaaaaatcgaaattttagaatttttctaaaatcggtagttttcgaaataaaataaaaatgttattttaaaaattattttaaaaaatttcgagaaattcaaaaatcgaacagaaatgttcgattttttgctacagtgcattttttttccacttctacgactttaaaggggggcgcatttatgcggaagggtcttgccgtgcacatagtcatcatttttaacaaagtctgctcaaaattcgcggagatcacgcgtagatcacaattaatttgtgaaaaagcaacagaaatacgaaatatgggataaatattttgtgatcttcatgtgatctacgcgaattttacacagaaactgctaaaaatgatgactaaatgcgcggcaagacccttccgcataaatgctcccccctttaaagtcgtagaagtaggaaaaaatgcactgtatggtgaatttgaaaattttctaaaaatccgaataatttagtatattggggtttcgacgaaaaatgccaatttttcagaaaaaaaaaaaatccttttccgagttttttcgttattttttctaaactcacagtatattagcgaattttcaacaaattcgacaaaaaattctgactgttttctagaaaaaaaaaaaggcggcatgcgcaagtttcaaaatttcccccccccccccttaaattaataacaaaactgggagatatatcttt';
   
4. $s ~~ m:ov/(.**8){%h{$0}++}/;
   
5. .say for %h.sort;

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zhagnqiang829

看不懂，要在wondos下运行。
$s ~~ mv什么意思？
运行出错，是不要安装某个模块呀？
谢谢
回复 3# rubyish


  

yinyuemi

1. perl -le '$str="gtatagaaatcatcgatttttcaggaaaagcaagaaagatcggtttaaaaaattatgaaattttattttaaaaatcgaaaaatcaacaaaaaaaatcgaaattttagaatttttctaaaatcggtagttttcgaaataaaataaaaatgttattttaaaaattattttaaaaaatttcgagaaattcaaaaatcgaacagaaatgttcgattttttgctacagtgcattttttttccacttctacgactttaaaggggggcgcatttatgcggaagggtcttgccgtgcacatagtcatcatttttaacaaagtctgctcaaaattcgcggagatcacgcgtagatcacaattaatttgtgaaaaagcaacagaaatacgaaatatgggataaatattttgtgatcttcatgtgatctacgcgaattttacacagaaactgctaaaaatgatgactaaatgcgcggcaagacccttccgcataaatgctcccccctttaaagtcgtagaagtaggaaaaaatgcactgtatggtgaatttgaaaattttctaaaaatccgaataatttagtatattggggtttcgacgaaaaatgccaatttttcagtaatttctggtcttttctaaaaaaatctacatatttcagatctcttcctccttttccgagttttttcgttattttttctaaactcacagtatattagcgaattttcaacaaattcgacaaaaaattctgactgttttctagaaaaaaaaaaaggcggcatgcgcaagtttcaaaatttgccgcacacctctgggcattaccttgaaagtatcaatggaaaagtgtcgcaagatttaattttctgatattccccccccccctcccgttttacttgtttctaggtttgagtttacttaaattaataacaaaactgggagatatatgctcgaaaattagacagaatctctgcctggacgatttctaggctacgccgtcattcccatagttttcataatctttcggctcagtgatcgaa"; while($str=~m{.{8}}g){$hash{$&}++;pos($str)-=7};use Data::Dumper;print Dumper \%hash'

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zhagnqiang829

谢谢你，运行速度很快，就是结果的形式我怎么改也分不开？
#!usr/bin/perl -w
#use strict;
use Data:umper;
open IN,"data.txt";
open OUT,">result.txt";
$str=<IN>;
while($str=~m{.{8}}g){


$hash{$&}++;
pos($str)-=7
}
print  OUT Dumper \%hash

结果形式
$VAR1 = {
          'cacacctc' => 1,
          'cggagatc' => 1,
          'cggctcag' => 1,
          'gcaagatt' => 1,
          'gtgatctt' => 1,
          'ctggacga' => 1,
          'atttaatt' => 1,
          'cgtagatc' => 1,
          'cttttccg' => 1,
          'ggctacgc' => 1,
          'aggggggc' => 1,
          'tattttaa' => 3,
          'aatgctcc' => 1,
          'tctaaaat' => 1,
          'caacagaa' => 1,
          'acaaaaaa' => 2,
          'agaaatac' => 1,
          'ccgaataa' => 1
        };
最好是：
       cacacctc     1
          cggagatc   1
          cggctcag   1
          gcaagatt   1
          gtgatctt    1
          ctggacga   1
          atttaatt     1
          cgtagatc    1
          cttttccg     1
          ggctacgc   1
         aggggggc   1
          tattttaa     3
          aatgctcc    1
         
回复 5# yinyuemi


   

yinyuemi

回复 6# zhagnqiang829


    map{print $_,"\t",$hash{$_},"\n"}keys %hash

zhagnqiang829

OK
多谢。。回复 7# yinyuemi


   

txh_zyy

学习，感谢回复 5# yinyuemi


   

rubyish

优化下:

1. #!/usr/bin/perl
   
2. 
   
3. use 5.016;
   
4. use threads;
   
5. 
   
6. open my $d, 'datafile';
   
7. my $s = <$d>;
   
8. chomp $s;
   
9. my ( $p, $ta, $x, $in, @th ) = ( 20, '', 0 );
   
10. my $i = int( length($s) / $p ) + 1;
    
11. 
    
12. for ( 1 .. $p ) {
    
13.     my $sp = substr( $s, $x, $i );
    
14.     $x += $i;
    
15.     $in = $ta . $sp;
    
16.     push @th, threads->create( \&that );
    
17.     $ta = substr( $sp, -7, 7 );
    
18. }
    
19. 
    
20. my ( @r, %k );
    
21. push @r, $_->join for @th;
    
22. 
    
23. for (@r) {
    
24.     my %h = %$_;
    
25.     $k{$_} += $h{$_} for keys %h;
    
26. }
    
27. 
    
28. say "$_\t$k{$_}" for sort keys %k;
    
29. 
    
30. sub that {
    
31.     my %h;
    
32.     for ( 0 .. length($in) - 8 ) {
    
33.         $h{ substr( $in, $_, 8 ) }++;
    
34.     }
    
35.     return \%h;
    
36. }

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