I'm not sure I understand your specification as to what the conditions are for "captures the hairpin best", but as I understand it, it has something to do with how the ranges overlap? In that case, here are some threads that might be of interest: Calculate the overlap length between two ranges, Range overlap (with a lot of ranges), or finding intermediate range values from two file columns (in the latter I mention Interval trees, which might be useful here). If your input data is large, that might mean you need a different data structure for efficient lookups.

As for reading the file into a data structure, that's probably easiest with a simple state machine type approach, in this example I'm keeping the state (the current key) as $curkey:

use warnings;
use strict;
use Data::Dump;

my %hash;
my $curkey;
while (<DATA>) {
    chomp;
    if (/^>(\w+)$/) {
        $curkey = $1;
    }
    elsif ( my ($data,$low,$high) =
        /^\s*(\w+)\s+(\d+)\s*\.\.\s*(\d+)\s*$/ ) {
            die "value seen before header: '$_'"
                unless defined $curkey;
            push @{ $hash{$curkey} },
                { data=>$data, low=>$low, high=>$high };
    }
    else { die "don't know how to parse: '$_'" }
}
dd \%hash;

__DATA__
>key1
Foo  10 .. 20
Bar  11 .. 21
>key2
Quz  30 .. 40
Baz  37 .. 45

[download]

Update: Minor tweaks to regex and text.

In reply to Re: Making use of a hash of an array... by haukex
in thread Making use of a hash of an array... by Peter Keystrokes

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