I have a file with two tab-separated columns. The first column contains IDs and the second column contains corresponding values.
I need to sort the IDs based on their corresponding values. After sorting, I want to divide the IDs into four ranges: highly expressed, moderately expressed, lowly expressed, and non-expressed.
To determine the expression ranges, I will set the value of non-expressed genes to 0. Then, I will sort the remaining values from high to low and equally divide them into three parts. Finally, I will report the four parts in separate files.
Following is a Perl script to accomplish this task:

open FA,"$ARGV[0]";

while(<FA>){
chomp;
($gene_id,$tpm)=split /\t/,$_;

if ($tpm >1){
push @tpm,$tpm;
}
else{

push @non_expressed,$tpm
}
}

@tpm=sort {$b <=>$a} @tpm;

@non_expressed =sort {$b <=>$a}  @non_expressed;

$n=scalar @tpm;
#print"$n\n";
$num1=int($n/4);

$top=@tpm[$num1];

$middle1=@tpm[$num1+1];
$middle2=@tpm[$num1*3];

$end=@tpm[$num1*3+1];

#print"$num1\t $top\t$middle1\t$middle2\t$end\n";




open FA,"$ARGV[0]";

while(<FA>){
    chomp;
    ($gene_id,$tpm)=split /\t/,$_;
    if($gene_id eq 'gene_id'){next;}
    if($tpm > $top){
        push @top_id,$gene_id;
        }   

    elsif($middle1>$tpm  and  $middle2<$tpm){
        push @mid_id,$gene_id;

        }

    elsif($tpm< $end and $tpm >=1){

        push @end_id,$gene_id;

        }

    elsif($tpm >= 0 and $tpm <1){
        push @nonexpress_id,$gene_id;

        }


    }

open OU1,">$ARGV[1]";

foreach(@top_id){
    print OU1  "$_\n";

    }

open OU2,">$ARGV[2]";

foreach(@mid_id){
    print OU2 "$_\n";
    }



open OU3,">$ARGV[3]";

foreach(@end_id){
    print OU3 "$_\n";
    }


open OU4,">$ARGV[4]";

foreach(@nonexpress_id){
    print OU4 "$_\n";
    }

To use this Perl script, follow these steps:

perl   perl_sort.pl     average_CK_TPM.txt     high.txt    mid.txt    low.txt    Non.txt