Question

I am back with another question. I have a list of data:

1 L DIELTQSPE H EVQLQESDAELVKPGASVKISCKASGYTFTDHE
2 L DIVLTQSPRVT H EVQLQQSGAELVKPGASIKDTY
3 A ALQLTQSPSSLSAS B RITLKESGPPLVKPTCS C ELDKWAN
4 A ALQLTQSPSSLSAS B RITLKESGPPLVKPTCS C ELDKWAG
5 A ALQLTQSPSSLSAS B RITLKESGPPLVKPTCS C LELDKWASL
6 L DIQMTQIPSSLSASLSIC H EVQLQQSGVEVKMSCKASGYTFTS
7 L SYELTQPPSVSVSPGSIT H QVQLVQSAKGSGYSFS P YNKRKAFYTTKNIIG
8 L SYELTQPPSVSVSPGRIT H EVQLVQSGAASGYSFS P NNTRKAFYATGDIIG
9 A MPIMGSSVAVLAIL B DIVMTQSPTVTI C EVQLQQSGRGP
10 A MPIMGSSVVLAIL B DIVMTQSPTVTI C EVQLQQSGRGP
11 L DVVMTQTPLQ H EVKLDESVTVTSSTWPSQSITCNVAHPASSTKVDKKIE
12 A DIVMTQSPDAQYYSTPYSFGQGTKLEIKR

And I would like to compare the 3rd elements && 5th elements of each row, then group them if they have the same 3rd && 5th elements.
For example, with the data above, the results will be :

3: 3 A ALQLTQSPSSLSAS B RITLKESGPPLVKPTCS C ELDKWAN
   4 A ALQLTQSPSSLSAS B RITLKESGPPLVKPTCS C ELDKWAG
   5 A ALQLTQSPSSLSAS B RITLKESGPPLVKPTCS C LELDKWASL
9: 9 A MPIMGSSVAVLAIL B DIVMTQSPTVTI C EVQLQQSGRGP
   10 A MPIMGSSVVLAIL B DIVMTQSPTVTI C EVQLQQSGRGP

Fyi, in the actual data, the 3rd, 5th, 7th elements are very long. I have made them cut to see the whole.

This is what I have done, I know it is very clumsy, but as a beginner, I am doing my best.
And the problem is that it shows only the first set of ‘same’ group.
Could you show me where it went wrong and/or other pretty methods to solve this, please?

my $file = <>;
open(IN, $file)|| die "no $file: $!\n";
my @arr;
while (my $line=<IN>){
        push @arr, [split (/\s+/, $line)] ;
}
close IN;

my (@temp1, @temp2,%hash1);
for (my $i=0;$i<=$#arr ;$i++) {
    push @temp1, [$arr[$i][2], $arr[$i][4]]; 
    for (my $j=$i+1;$j<=$#arr ;$j++) {
        push @temp2, [$arr[$j][2], $arr[$j][4]];
        if (($temp1[$i][0] eq $temp2[$j][0])&& ($temp1[$i][1] eq $temp2[$j][1])) {
            push @{$hash1{$arr[$i][0]}}, $arr[$i], $arr[$j];
        }
    }
}
print Dumper \%hash1;

Answer 1

You appear to have overcomplicated this a bit more than it needs to be, but that’s common for beginners. Think more about how you would do this manually:

• Look at each line.
• See whether the third and fifth fields are the same as the previous line.
• If so, print them.

The looping and all that is completely unnecessary:

#!/usr/bin/env perl

use strict;
use warnings;

my ($previous_row, $third, $fifth) = ('') x 3;

while (<DATA>) {
  my @fields = split;
  if ($fields[2] eq $third && $fields[4] eq $fifth) {
    print $previous_row if $previous_row;
    print "\t$_";
    $previous_row = '';
  } else {
    $previous_row = $fields[0] . "\t" . $_;
    $third = $fields[2];
    $fifth = $fields[4];
  }
}

__DATA__
1 L DIELTQSPE H EVQLQESDAELVKPGASVKISCKASGYTFTDHE
2 L DIVLTQSPRVT H EVQLQQSGAELVKPGASIKDTY
3 A ALQLTQSPSSLSAS B RITLKESGPPLVKPTCS C ELDKWAN
4 A ALQLTQSPSSLSAS B RITLKESGPPLVKPTCS C ELDKWAG
5 A ALQLTQSPSSLSAS B RITLKESGPPLVKPTCS C LELDKWASL
6 L DIQMTQIPSSLSASLSIC H EVQLQQSGVEVKMSCKASGYTFTS
7 L SYELTQPPSVSVSPGSIT H QVQLVQSAKGSGYSFS P YNKRKAFYTTKNIIG
8 L SYELTQPPSVSVSPGRIT H EVQLVQSGAASGYSFS P NNTRKAFYATGDIIG
9 A MPIMGSSVAVLAIL B DIVMTQSPTVTI C EVQLQQSGRGP
10 A MPIMGSSVAVLAIL B DIVMTQSPTVTI C EVQLQQSGRGP
11 L DVVMTQTPLQ H EVKLDESVTVTSSTWPSQSITCNVAHPASSTKVDKKIE
12 A DIVMTQSPDAQYYSTPYSFGQGTKLEIKR

(Note that I changed line 10 slightly so that its third field will match line 9 in order to get the same groups in the output as specified.)

Edit: One line of code was duplicated by a copy/paste error.

Edit 2: In response to comments, here’s a second version which doesn’t assume that the lines which should be grouped are contiguous:

#!/usr/bin/env perl

use strict;
use warnings;

my @lines;
while (<DATA>) {
  push @lines, [ $_, split ];
}

# Sort @lines based on third and fifth fields (alphabetically), then on
# first field/line number (numerically) when third and fifth fields match
@lines = sort { 
  $a->[3] cmp $b->[3] || $a->[5] cmp $b->[5] || $a->[1] <=> $b->[1] 
} @lines;

my ($previous_row, $third, $fifth) = ('') x 3;
for (@lines) {
  if ($_->[3] eq $third && $_->[5] eq $fifth) {
    print $previous_row if $previous_row;
    print "\t$_->[0]";
    $previous_row = '';
  } else {
    $previous_row = $_->[1] . "\t" . $_->[0];
    $third = $_->[3];
    $fifth = $_->[5];
  }
}

__DATA__
1 L DIELTQSPE H EVQLQESDAELVKPGASVKISCKASGYTFTDHE
3 A ALQLTQSPSSLSAS B RITLKESGPPLVKPTCS C ELDKWAN
2 L DIVLTQSPRVT H EVQLQQSGAELVKPGASIKDTY
5 A ALQLTQSPSSLSAS B RITLKESGPPLVKPTCS C LELDKWASL
7 L SYELTQPPSVSVSPGSIT H QVQLVQSAKGSGYSFS P YNKRKAFYTTKNIIG
6 L DIQMTQIPSSLSASLSIC H EVQLQQSGVEVKMSCKASGYTFTS
9 A MPIMGSSVAVLAIL B DIVMTQSPTVTI C EVQLQQSGRGP
8 L SYELTQPPSVSVSPGRIT H EVQLVQSGAASGYSFS P NNTRKAFYATGDIIG
11 L DVVMTQTPLQ H EVKLDESVTVTSSTWPSQSITCNVAHPASSTKVDKKIE
10 A MPIMGSSVAVLAIL B DIVMTQSPTVTI C EVQLQQSGRGP
12 A DIVMTQSPDAQYYSTPYSFGQGTKLEIKR
4 A ALQLTQSPSSLSAS B RITLKESGPPLVKPTCS C ELDKWAG