求解 如何输出文件中某一列长度最长的行？

niuguohao

我有一个基因组文件，其中第一列是染色体名称，第十列是对应的序列，目的是输出 在第一列名称相同的条件下，第十列长度最长的行。

文件大致如下：

EAA1-10       0       scaffold1478    495341  60      24S4359M126I10900M64I917M65I2319M       *       0       0       AATTGGAACGAAATAATTGGAACGAAATAATTGGAACGAAAT
EAA1-10       0       scaffold1478    495341  60      24S4359M126I10900M64I917M65I2319M       *       0       0       AATTGGAACGAAATAATTGGAACGAAAT
EAA1-11       0       scaffold147    495341  60      24S4359M126I10900M64I917M65I2319M       *       0       0       AATTGGAACGAAATAATTGGAACGAAATAATTGGAACGAAAT
EAA1-12       0       scaffold100    495341  60      24S4359M126I10900M64I917M65I2319M       *       0       0       AATTGGAACGAAATAATTGGAACGAAATTGGAACGAAATAATGGAACGAAA
...

请求各位大神指教~

stanley_tam

这样？

1. #!perl6
   
2. use v6.c;
   
3. 
   
4. sub MAIN {
   
5.     my $input_file = 'a.txt';
   
6.     my %chromosome_hash = %();
   
7.     for $input_file.IO.open(:chomp).lines -> $line {
   
8.         my @parts = $line.split(/\s+/);
   
9.         my $name = @parts[0];
   
10.         my $current_seq_length = @parts[9].chars;
    
11. 
    
12.         if %chromosome_hash{$name}<length>:exists {
    
13.             my $seq_length = %chromosome_hash{$name}<length>;
    
14.             if $current_seq_length > $seq_length {
    
15.                 %chromosome_hash{$name}<length> = $current_seq_length;
    
16.             }
    
17.         }
    
18.         else {
    
19.             %chromosome_hash{$name}<length> = $current_seq_length;
    
20.         }
    
21.         %chromosome_hash{$name}<line> = $line;
    
22.     }
    
23. 
    
24.     for %chromosome_hash.values.sort -> $value_hash {
    
25.         $value_hash<line>.say;
    
26.     }
    
27. }
    

复制代码

niuguohao

回复 2# stanley_tam

非常感谢！！
我大约看明白您的意思了，但是运行出现了报错：
Scalar value @parts[0] better written as $parts[0] at delete.pl line 10.
Scalar value @parts[9] better written as $parts[9] at delete.pl line 11.
"my" variable %chromosome_hash masks earlier declaration in same scope at delete.pl line 16.
"my" variable $name masks earlier declaration in same scope at delete.pl line 16.
"my" variable $current_seq_length masks earlier declaration in same scope at delete.pl line 16.
"my" variable %chromosome_hash masks earlier declaration in same scope at delete.pl line 20.
"my" variable $name masks earlier declaration in same scope at delete.pl line 20.
"my" variable $current_seq_length masks earlier declaration in same scope at delete.pl line 20.
"my" variable %chromosome_hash masks earlier declaration in same scope at delete.pl line 22.
"my" variable $name masks earlier declaration in same scope at delete.pl line 22.
"my" variable %chromosome_hash masks earlier declaration in same scope at delete.pl line 25.
Warning: Use of "values" without parentheses is ambiguous at delete.pl line 25.
syntax error at delete.pl line 7, near "%() "
syntax error at delete.pl line 8, near "$input_file."
Global symbol "%line" requires explicit package name at delete.pl line 8.
syntax error at delete.pl line 13, near "if %chromosome_hash"
syntax error at delete.pl line 13, near "<length>:"
Execution of delete.pl aborted due to compilation errors.

stanley_tam

要安装perl6

1. https://perl6.org/downloads/

复制代码

niuguohao

回复 4# stanley_tam
我安装失败了，最后一步make install 这里总是有问题，请问大神如果用perl5的话，是不是要改这种中间带点的行啊
for $input_file.IO.open(:chomp).lines -> $line {

b114213903

1. 
   
2. my $Flag={};
   
3. my $Data={};
   
4. while(my $line=<DATA>){
   
5.         chomp;
   
6.         my($id,$seq)=(split(/\s+/,$line))[0,-1];
   
7.         my $length=length($seq);
   
8.         if($Flag->{$id}){
   
9.                 if($length>$Flag->{$id}){
   
10.                         $Flag->{$id}=$length;
    
11.                         $Data->{$id}=$line;
    
12.                 }
    
13.         }else{
    
14.                 $Flag->{$id}=$length;
    
15.                 $Data->{$id}=$line;
    
16.         }
    
17. }
    
18. foreach my $id (sort keys %{$Data}){
    
19.         print "$Data->{$id}\n";
    
20. }
    
21. 
    
22. 
    
23. __DATA__
    
24. EAA1-10       0       scaffold1478    495341  60      24S4359M126I10900M64I917M65I2319M       *       0       0       AATTGGAACGAAATAATTGGAACGAAATAATTGGAACGAAAT
    
25. EAA1-10       0       scaffold1478    495341  60      24S4359M126I10900M64I917M65I2319M       *       0       0       AATTGGAACGAAATAATTGGAACGAAAT
    
26. EAA1-11       0       scaffold147    495341  60      24S4359M126I10900M64I917M65I2319M       *       0       0       AATTGGAACGAAATAATTGGAACGAAATAATTGGAACGAAAT
    
27. EAA1-12       0       scaffold100    495341  60      24S4359M126I10900M64I917M65I2319M       *       0       0       AATTGGAACGAAATAATTGGAACGAAATTGGAACGAAATAATGGAACGAAA
    

复制代码

ramsay_dan

  1 #!/usr/bin/perl -w
  2 use strict;
  3 use 5.010;
  4
  5 open my $IN_1 , '<' , "orange_in_1.file" or die "can not read! $!\n";
  6 open my $OUT  , '>' , "orange_out.file"  or die "can not write! $!\n";
  7
  8 my %hash;
  9 my @line;
10 while (<$IN_1>) {
11 chomp;
12 @line = split /\s+/;
13 if (exists $hash{$line[0]}) {
14     if (length ($hash{$line[0]}->[8]) < length ($line[9])) {
15     $hash{$line[0]}->[0] = $line[1];
16     $hash{$line[0]}->[1] = $line[2];
17     $hash{$line[0]}->[2] = $line[3];
18     $hash{$line[0]}->[3] = $line[4];
19     $hash{$line[0]}->[4] = $line[5];
20     $hash{$line[0]}->[5] = $line[6];
21     $hash{$line[0]}->[6] = $line[7];
22     $hash{$line[0]}->[7] = $line[8];
23     $hash{$line[0]}->[8] = $line[9];
24 }
25 } else {$hash{$line[0]} = [$line[1], $line[2], $line[3], $line[4], $line[5], $line[6], $line[7], $line[8], $line[9]];}
26 }
27
28 map {print $OUT "$_ $hash{$_}->[0] $hash{$_}->[1] $hash{$_}->[2] $hash{$_}->[3] $hash{$_}->[4] $hash{$_}->[5] $hash{$_}->[6] $hash{$_}->[7] $hash{$_}->[8]\n";} sort keys %hash;
运行结果：见附件图片

ramsay_dan

回复 6# b114213903

学习学习！

灿烂小猪

回复 6# b114213903