A oneliner sounds like an invitation..

#warning windows double quotes
perl -lanE "print $F[0],qq(\t)x($F[3]=~/Pro/?1:$F[3]=~/Bact/?2:3),$F[4
+]" genetable.txt

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]

L*

update if also want the headers printed you can use them to match: 

perl -lanE "BEGIN{@h=qw(Gene Prot_Ente Bact_Bact Firm_Lach);print join
+ qq(\t),@h}
            print $F[0],qq(\t)x($F[3]=~/$h[1]/?1:$F[3]=~/$h[2]/?2:3),$
+F[4]" genetable.txt

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]
There are no rules, there are no thumbs..
Reinvent the wheel, then learn The Wheel; may be one day you reinvent one of THE WHEELS.

In reply to Re: creating a matrix like format -- oneliner by Discipulus
in thread creating a matrix like format by perl_user123

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