Update 3:
Thanks a lot to everyones VERY useful comments which are valid and constructive. I am going to work on the code for a bit and once I get it working will come back for more detailed help if appropriate.

Thanks again for everyones generous time and help.....

Update2:
I think I got something working can someone check if its OK? Its working but not sure if its the most efficient?

Thanks again for everyones help, spologizies for all the questions.

Dave

#!/usr/bin/perl

open(FILE, "args.test");

@files=<FILE>;

my @allfiles;
for my $filename(@files){
    open FILE, $filename ||
        die "Cannot open $filename for reading: $!\n";
    push @allfiles, <FILE>;
    close FILE;
}

@test=grep /chr1:8325525/,@allfiles;

print "@test\n";

[download]
Update Thanks for everyones comment so far, can someone give me some pointers to how to Array of Arrays or a Hash of Arrays from 100 files or point me to some code that does this... Thanks again. Hi everyone If I had say 100 files and I want to put each file into an array into memory like below. But how do I automatically create the name for each array so that I have 50 unique names? I can then get each array to spit out the data eg: Thank you for your help! 
print "$array[1],$array2[1],$array3[1],$array4[1]...etc\/n";

[download]


while(<FILES>){
chomp;

process_into_array($_);


}

sub process_into_array{
my $file=shift;


open(DAT, $file);
@file=(<DAT>);

}

[download]

In reply to slurping many Arrays into memory...Please Help by david_lyon

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