Dear Monks,

I have a file in the following format: 

ENSG00000088992 TESC    1105894 Prot_Ente       0.31       0.038
ENSG00000105374 NKG7    1105894 Prot_Ente       0.37        0.01
ENSG00000005810 MYCBP2  4322986 Bact_Bact       0.29       0.044
ENSG00000088992 TESC    4322986 Bact_Bact       0.27       0.044
ENSG00000109016 DHRS7B  4322986 Bact_Bact       -0.37      0.008
ENSG00000069248 NUP133  364926  Bact_Bact       0.32       0.024
ENSG00000005810 MYCBP2  363400  Firm_Lach       -0.29      0.036
ENSG00000105374 NKG7    363400  Firm_Lach       -0.27      0.047
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

[download]

From this table I want to create a matrix where 1st column becomes the row names and 4th column becomes the column names. The values in the 5th column fill in the matrix. Something like this: 

Gene            Prot_Ente Bact_Bact Firm_Lach 
ENSG00000088992 0.31
ENSG00000105374 0.37
ENSG00000005810            0.29
ENSG00000088992            0.27 
ENSG00000109016           -0.37 
ENSG00000069248            0.32 
ENSG00000005810                      -0.29 
ENSG00000105374                      -0.27
ENSG00000105374                      -0.27
ENSG00000105374                      -0.30 
ENSG00000133107            0.35

[download]

Following is the code that I am using and it is not working correctly. Not all the values of the 5th column are printed because of the redundant keys in the nested hashes that I am using. 

$file=$ARGV[0];
open(FH,$file);
open OUT1,">./$file\_rho_temp";
while(<FH>){
           chomp;
           next if($_=~/^Gene/);
           @arr=split(/\s+/,$_);
                $rhash{$arr[0]}{$arr[3]}=$arr[4];

}

@keys = keys %{$rhash{(keys %rhash)[0]}};
$format = "%1s  " . ("%2s       " x @keys) . "\n";
printf OUT1 $format, "Genes", @keys;
foreach $key (keys %rhash) {
printf OUT1 $format, $key, @{$rhash{$key}}{@keys};
}

[download]

Can someone suggest some modification in this code or another method to make this work? Thanks a lot in advance.

In reply to creating a matrix like format by perl_user123

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