Hi guys, I basically have 2 arrays(populated from input file) and all i have to do is, search the values from one array and see if it is there in the other and record the no of occurrences as well. my main query array has 375 values and my other search array has 73372 values. so the number of searches totally will be 27514500 on the worst case and it taking ages to finish running the program. I do have to also include more functions to this script and im afraid how long that is going to take more. Please advice me why my program is so slow and any other alternative ideas that i could use. 
sample values of @gl
CD9
TBN
NANOG
KITL
FUT4
SALL4
MYC
STAT3
ESRRB
AKP2
SOX2
POU5F1
KLF4

[download]
sample of @hfr_genes
LYPLA1
LYPLA1
LYPLA1
LYPLA1
LYPLA1
LYPLA1
LYPLA1
LYPLA1
LYPLA1
LYPLA1

[download]
my code:
do
{
    if( my$index_gl=grep{$hfr_genes[$_]=~/^$gl[$index]$/}0..$#hfr_gene
+s)
    {
        print TEST "Val $gl[$index] is present $index_gl times\n";
        $index++;
    }
    else
    {
        
        $index++;
    }
}
until ($index==(scalar(@hfr_genes)));

[download]
please help! thanks

In reply to A better way to make the script run faster? by rocketperl

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