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

...
} @genes;

print "Gene", $_+1, " @{$gene_matrix[$_]}\n" for 0 .. $#gene_matrix;

Gene1 1 0 0
Gene2 1 1 0
...
Gene4 0 1 1
Gene5 0 0 1
Gene6 0 0 0

<code>
[shift-insert, to paste output from my terminal]
</code>

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

...
    [ map { ~~exists $_->{$gene} } @in_file ]
  } @{+shift};
}->( \@raw_files, \@genes );