I tried the code and it works perfect!
One last question though:
Suppose you have this list:
HIT:PF12951 SEQ_START:120  SEQ_END:350
HIT:PF03797 SEQ_START:822   SEQ_END:1073
HIT:PF15789 SEQ_START:1515   SEQ_END:1547
HIT:PF00267 SEQ_START:1200   SEQ_END:1350

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where there are codes not only before but also after the wanted one (PF03797). In this case the desired range would be between 351-1199 (350 is the end of the previous element and 1200 is the start of the next element).
How can I take both of them? I tried the following without success
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) 
    {
        my $start;
        my $end;
        #print $data[$i][0]."\n";
        if ($special{$data[$i][0]}) 
        {
            print $data[$i][2]."\n";
            if($start=$i)
            {
                $start = $data[$i - 1][2] - 1;
            }
            else
            {
                $start = $data[$i][1] - 1;
            }

            if($end=$i)
            {
                $end = $data[$i][2] - 1;
            }
            else
            {
                $end = $data[$i + 1][1] - 1;
            }
            print join "\t" => $id, $data[$i][0], $start, $end;
        }
    }
}
}
print "\n";
__DATA__
ID:A0AWZ5
HIT:PF12951 SEQ_START:120  SEQ_END:350
HIT:PF03797 SEQ_START:822   SEQ_END:1073
HIT:PF15789 SEQ_START:1515   SEQ_END:1547
HIT:PF00267 SEQ_START:1200   SEQ_END:1350
//

[download]

In reply to Re^3: Stuck in my final step of code using array of arrays by Anonymous Monk
in thread Stuck in my final step of code using array of arrays by Anonymous Monk

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