#! perl -slw
use strict;
use Data::Dump qw[ pp ];

my %data;
while( <DATA> ) {
    my( $str, @values ) = map{ s[^\s+|\s+$][]g; $_ } split "\t";
    $data{ $str } = [ map [ split ' ' ], @values ];
}

pp %data;

my @output;
while( my( $key, $valueRef ) = each %data ) {
    my @required;
    for my $c ( 0 .. length( $key ) - 1 ) {
	push @required, $valueRef->[ $c ][ index "ACGT", substr $key, $c, 1 ];
    }
    push @output, \@required;
}

pp \@output;

__DATA__
AGAC 	 9 -29 -39 -37 	 27 -28 -39 -37 	 26 -27 -39 -37 	 27 -27 -39 12
ACGT 	 1 -2 3 -4 	 5 -6 7 -8 	 9 -10 11 -12 	 13 -14 15 -16

##</code><code>##

c:\test>junk6
(
  "AGAC",
  [
    [9, -29, -39, -37],
    [27, -28, -39, -37],
    [26, -27, -39, -37],
    [27, -27, -39, 12],
  ],
  "ACGT",
  [
    [1, -2, 3, -4],
    [5, -6, 7, -8],
    [9, -10, 11, -12],
    [13, -14, 15, -16],
  ],
)

[[9, -39, 26, -27], [1, -6, 11, -16]]

##</code><code>##

#! perl -slw
use strict;
use Data::Dump qw[ pp ];

my %data;
while( <DATA> ) {
    my( $str, @values ) = map{ s[^\s+|\s+$][]g; $_ } split '<TAB>';
    $data{ $str } = [ map [ split ' ' ], @values ];
}

pp %data;

my @output;
while( my( $key, $valueRef ) = each %data ) {
    my @required;
    for my $c ( 0 .. length( $key ) - 1 ) {
	push @required, $valueRef->[ $c ][ index "ACGT", substr $key, $c, 1 ];
    }
    push @output, \@required;
}

pp \@output;

__DATA__
AGAC <TAB> 9 -29 -39 -37 <TAB> 27 -28 -39 -37 <TAB> 26 -27 -39 -37 <TAB> 27 -27 -39 12
ACGT <TAB> 1 -2 3 -4 <TAB> 5 -6 7 -8 <TAB> 9 -10 11 -12 <TAB> 13 -14 15 -16