i'm not sure if i get the problem right but this script will find the min of all values in column 2 of all given files and the max of all values in column 3.

you just call it with the file names as arguments.

#!/usr/bin/perl -w

use strict;

my $min = undef;
my $max = undef;
foreach (@ARGV) {
    open(F, "< $_");
    while(my $line = <F>) {
        chop($line);
        $line =~ s/[\ \t]+/:/g;
        my @p = split(/:/,$line);
        if(!defined($min)) {
            $min = $p[1];
        }
        if(!defined($max)) {
            $max = $p[2];
        }
        if($p[1] < $min) {
            $min = $p[1];
        }
        if($p[2] > $max) {
            $max = $p[2];
        }
    }
    close(F);
}
print "$min $max\n";
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#!/usr/bin/perl -w

use strict;

my %minmax;


foreach (@ARGV) {
    open(F, "< $_");
    while(my $line = <F>) {
        chop($line);
        my @p = split(/\t/,$line);

        if(!exists( $minmax{ $p[0] }{ min } )) {
            $minmax{ $p[0] }{ min } = $p[1];
        }
        if($p[1] < $minmax{ $p[0] }{ min }) {
            $minmax{ $p[0] }{ min } = $p[1];
        }

        if(!exists( $minmax{ $p[0] } { max } )) {
            $minmax{ $p[0] }{ max } = $p[2];
        }
        if($p[2] > $minmax{ $p[0] }{ max }) {
            $minmax{ $p[0] }{ max } = $p[2];
        }

    }
    close(F);
}
foreach (keys %minmax) {
    print "$_: min: $minmax{$_}{min} max: $minmax{$_}{max}\n";
}
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file1:

chr1    4   60
chr2    2   40
chr3    4   90
chr1    5   40
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chr2    1   30
chr1    6   20
chr4    9   100
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chr1    2   20
chr2    2   90
chr1    6   20
chr4    4   30
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chr2    4   90
chr3    3   90
chr2    4   90
chr4    3   90
chr2    4   30
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chr1: min: 2 max: 60
chr2: min: 1 max: 90
chr3: min: 3 max: 90
chr4: min: 3 max: 100
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Your solution is an excellent use of a HoH! Here are a few items to consider within your foreach:

foreach (@ARGV) {
    open my $fh, '<', $_ or die $!;
    while ( my $line = <$fh> ) {
        next unless my @p = $line =~ /^(chr.+?)\t+(\d+)\t+(\d+)/;

        $minmax{ $p[0] }{min} //= $p[1];
        $minmax{ $p[0] }{max} //= $p[2];

        if ( $p[1] < $minmax{ $p[0] }{min} ) {
            $minmax{ $p[0] }{min} = $p[1];
        }

        if ( $p[2] > $minmax{ $p[0] }{max} ) {
            $minmax{ $p[0] }{max} = $p[2];
        }
    }
    close $fh;
}
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• A three-argument open is used
• A lexically-scoped variable is used for the file handle
• or die $! checks for open errors
• The regex line:
• Skips possible comment and track definition lines in the BED files
• And then makes using chomp and split unnecessary
• Uses defined-or-equals (//=) to replace the !exists

Hope this is helpful.

Hi, Thank you for your answer, but this wasn't the problem. I dont want to find just the minima and maxima of a chromosome. I want to find the overlapping regions and find the minima and maxima of that. So when there are lines in the 4 files like this:

file1:
chr1    100    500
chr1    25      50
file2:
chr1    10       50
chr1    60       80
file3:
chr1    12       40
chr1    41       45
file4:
chr1     20      45
chr1     48      80
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The line of the first file does not overlap with the other 3 files, so i dont want to find the minima and maxima. I want to find only the minima and maxima of the regions in which the lines of all four files overlap each other. So the minima and maxima of the other regions in the files. Minima = 10 maxima = 80