When people say "placeholders" I think "printf"... So, a variant. That reads the file with small matrix line by line: 
use strict;
use warnings;

my @template = qw(
  rs12272511 rs7107801 rs11027752 rs12421837
);

my $small_matrix = <<'END';
             rs12272511 rs11027752 rs12421837
rs12272511  1.0 .844 .276
rs11027752  .267 1.0 -.980
rs12421837 -.876 .374 1.0
END

open my $fh, '<', \$small_matrix;

my %ids = map { $_ => 1 } split ' ', <$fh>;

my $fmt_id_present = join ' ', map $ids{$_} ? '%s' : '0',
  @template;
my $fmt_id_missing = join ' ', ('0') x @template;

$_ = "%s $_\n" for $fmt_id_present, $fmt_id_missing;

print "\t@template\n";

for (@template) {
    if ( $ids{$_} ) {
        printf $fmt_id_present, split ' ', <$fh>;
    }
    else {
        printf $fmt_id_missing, $_;
    }
}

[download]
if you find the line open my $fh, '<', \$small_matrix; strange: yes, you can open strings as files in Perl.

In reply to Re: combining multiple matrices with placeholders if row and column values in one matrix do not exist in another by Anonymous Monk
in thread combining multiple matrices with placeholders if row and column values in one matrix do not exist in another by mulder4786

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