Thanks for suggestions. This is what I have tried, but am not able to go past this. 
my $file = "LIST";
open (FH, "< $file") or die "Can't open $file for read: $!";
my @hsa_sub = <FH>;

for($x=0;$x<=$#hsa_sub;$x++)
{
    $s=$hsa_sub[$x];
    $sline=`cat siper_sub | grep -n $s`;
    `sed '/substrate/!d; /$s/!d;{n;p}' everything_hsa | grep -i produc
+t | awk {'print $2,$3,$4'} >> prodlist`
    
    my $fil = "prodlist";
    open (FH, "< $fil") or die "Can't open $fil for read: $!";
    my @prod.$s.$x = <FH>;

}

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In reply to Re^2: A complicated file parsing and 2D array/matrix problem. by zing
in thread A file parsing and 2D array/matrix problem. by zing

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