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ENSG00000088992 TESC    1105894 Prot_Ente       0.31       0.038
ENSG00000105374 NKG7    1105894 Prot_Ente       0.37        0.01
...
ENSG00000105374 NKG7    364736  Firm_Lach       -0.27      0.039
ENSG00000105374 NKG7    186735  Firm_Lach       -0.30       0.037
ENSG00000133107 TRPC4   4322986 Bact_Bact       0.35        0.01

Gene            Prot_Ente Bact_Bact Firm_Lach 
ENSG00000088992 0.31
...
ENSG00000105374                      -0.27
ENSG00000105374                      -0.30 
ENSG00000133107            0.35

$file=$ARGV[0];
open(FH,$file);
...
foreach $key (keys %rhash) {
printf OUT1 $format, $key, @{$rhash{$key}}{@keys};
}