I strongly recommend you:

I think this should be fairly close to what you want (and shows examples of all the recommendations I made above): 

#!/usr/bin/env perl -l

use strict;
use warnings;

my %special = (PF03797 => 1);

{
    local $/ = "//\n";

    while (<DATA>) {
        my ($id) = /^ID:(\w+)/;
        my @data;

        while (/HIT:(\w+).*?SEQ_START:(\d+).*?(\d+)/g) {
            push @data, [ $1, $2, $3 ];
        }

        @data = sort { $a->[2] <=> $b->[2] } @data;

        for my $i (0 .. $#data) {
            if ($special{$data[$i][0]}) {
                my $start = $i ? $data[$i - 1][2] + 1 : 'none';
                print join "\t" => $id, $data[$i][0], $start, $data[$i
+][2];
            }
        }
    }
} 

__DATA__
ID:A0AWZ5
HIT:PF12951 SCORE:40.0  EVALUE:2.2e-10  HMM_START:2 HMM_END:32  SEQ_ST
+ART:421   SEQ_END:455
HIT:PF03797 SCORE:130.7 EVALUE:3.6e-40  HMM_START:7 HMM_END:261 SEQ_ST
+ART:822   SEQ_END:1073
HIT:PF12951 SCORE:38.7  EVALUE:5.5e-10  HMM_START:1 HMM_END:32  SEQ_ST
+ART:515   SEQ_END:547
//

[download]

Output:

A0AWZ5    PF03797    548    1073

[download]

-- Ken

In reply to Re: Stuck in my final step of code using array of arrays by kcott
in thread Stuck in my final step of code using array of arrays by Anonymous Monk

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