Do you intend to use the other @fields array elements in some way or the other? or are you only splitting in order to access the $field[5] to check whether it is Withdrwan or Public? in both cases, you can get a better edge if you filter your lines first and then do things with the elements that constitute each line, this way, you have obtained the interesting lines (the ones that has 'withdrwan') and reduced your data file to a somewhat manageable chunk... Here in the code posted below is a more direct approach where I read the file a line at a time, used a look-ahead regular expression to check for incidence of 'Withdrwan' -regardless of case- and then transferred that line to another new file that has the same header information as the source file with the objective of only filtering entries where 'Withdrawn' has appeared in that particular line...

my $path = "C:/Documents and Settings/aldaihi/Desktop/Monks";
open (my $fh, '<',"$path/genes.txt") or die ("could not open file $!\n
+");
open (my $rfh,'>',"$path/results.txt") or die ("could not open file $!
+\n");

my $firstLine = <$fh>;
print $rfh $firstLine;
while(<$fh>){
        chomp;
        if(/(?=Withdrawn)/i){
                #U can do things to the line in here
                #.....
                # split or rearrange .. 
                # 
                print $rfh $_,"\n";  
                }
        }
[download]

a module like Text::Table can give you control over how your data is placed in columns without breaking your head on spacing issues...

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