my @genes = qw( Gene1 Gene2 Gene3 Gene4 Gene5 Gene6 );

my @raw_files
  = ( "Gene1 Gene2 Gene3", "Gene2 Gene3 Gene4", "Gene3 Gene4 Gene5" );

my $gene_num = 1;
print "Gene", $gene_num++, " @{$_}\n" for sub {
  my @in_file = map { { map { $_ => 0 } split " ", $_ } } @{+shift};
  map {
    my $gene = $_;
    [ map { ~~exists $_->{$gene} } @in_file ]
  } @{+shift};
}->( \@raw_files, \@genes );