2行列の列同期

見えるよりも少し複雑です。おそらく、より良い機能を提供するライブラリがあるでしょう（Perlには多くの数学ライブラリがあります）。

しかし、これはあなたが望む結果を得ることを可能にします。

#!/usr/bin/perl

use strict;
use warnings;


#read file 1
open( my $file1, "<", "data1.txt" ) or die $!;

my $header_line = <$file1>;
chomp($header_line);
my ( $column1, @headers1 ) = split( ' ', $header_line );

my %results;
my %headers_in_file1 = map { $_ => 1 } @headers1;

for (<$file1>) {
    my ( $column, @values ) = split;
    my %these_results;
    @these_results{@headers1} = @values;
    $results{$column}         = \%these_results;
}
close ( $file1);


#read file 2
open( my $file2, "<", "data2.txt" ) or die $!;
$header_line = <$file2>;
chomp($header_line);
my ( $column2, @headers2 ) = split( ' ', $header_line );

my %results2;
my %headers_in_file2 = map { $_ => 1 } @headers2;

for (<$file2>) {
    my ( $column, @values ) = split;
    my %these_results;
    @these_results{@headers2} = @values;
    $results2{$column}        = \%these_results;
}
close ( $file2 );

#figure out the columns in both
my %in_both;
foreach my $header ( @headers1, @headers2 ) {
    if (    $headers_in_file1{$header}
        and $headers_in_file2{$header} )
    {
        $in_both{$header}++;
    }
}

#sort out headers for output. 
my @output_headers = sort keys %in_both;

print join( " ", $column1, @output_headers ), "\n";
foreach my $row ( sort keys %results ) {
    print $row, " ";
    for my $header (@output_headers) {
        print $results{$row}{$header}, " ";
    }
    print "\n";
}

print "Second\n";
print join( " ", $column2, @output_headers ), "\n";
foreach my $row ( sort keys %results2 ) {
    print $row, " ";
    for my $header (@output_headers) {
        print $results2{$row}{$header}, " ";
    }
    print "\n";
}