As almut said, as the size of the file grows, so will the hashes. I came up with a solution that only keeps one query in a hash at a time. Then your entries won't accumulate in the hash.

foreach $Query ( keys (%hash2) )

It isn't necessary to loop over the keys in hash2. Just use the first loop and, in your print string, $hash2{$Query}[2] will display ok.

As others have noted, it's not clear why you want to re-assign all the values in the field when in a condition where you have a new max or min.

In your sample data, the only fields that changed were the start, end fields.

Chris

#!/usr/bin/perl
use strict;
use warnings;

my @cols = qw/ score start stop one two /;
my %line_before;

my ($query, @data) = split /\t/, <DATA>;
chomp $data[-1]; # last @data has a newline

@{ $line_before{$query} }{ @cols } = @data;
my ($min, $max) = @data[1, 2];

while (<DATA>) {
    chomp;
    my %current_line;
    
    ($query, @data) = split /\t/;
    @{ $current_line{$query} }{ @cols } = @data;
    
    # if the prior and current queries don't match
    if (! exists $line_before{ $query }) {
        print_record(\%line_before, \@cols);
               ($min, $max) = @{ $current_line{$query} }{ qw/ start st
+op / };
    }
    else {
        
        my $start = $current_line{ $query }{ start };
        if ($start < $min) {
            $min = $start;
        }
        else {
            $current_line{ $query }{ start } = $min;
        }
        
        my $stop = $current_line{ $query }{ stop };
        if ($stop > $max) {
            $max = $stop;
        }
        else {
            $current_line{ $query }{ stop } = $max;
        }
    }
    %line_before = %current_line;
    
    print_record(\%line_before, \@cols) if eof;
}

sub print_record {
    my ($rec, $cols) = @_;
    my ($query) = keys %$rec; # There is only 1 key
    print join("\t", $query, @{ $rec->{$query} }{ @$cols }), "\n";
}    

__DATA__
Books    6    159290954    159291342    +     Author
Books    6    159294558    159294653    +     Author
Books    6    159316253    159316398    +     Author
Books    6    159330999    159331385    +     Author
Books    6    159290971    159290997    +     Author
Books    6    159316253    159316398    +     Author
Books    6    159330999    159331289    +     Author
Books    6    159316268    159316398    +     Author
Books    6    159330999    159331245    +     Author
Coopy    1    123456789    987654321    +     Author
[download]

Output

C:\perlp>perl 814937.pl
Books   6       159290954       159331385       +        Author
Coopy   1       123456789       987654321       +        Author
[download]

Update: Captured 'query' in $query (and changes to array indices). Reset min - max when a record changed.

Update 2: I was 'assuming' the queries came in groups (that query only to appear in that bunch). Is that the case? Or, can they be interspersed.