Hi,
This is a working code which try to remove strings that contain poly-ATCG, i.e. remove the strings when the composition of A or T or C or G is greater than a threshold. So with the array below it'll return only "ATCGAT".

My code below although gives the correct result, somehow I feel it's clumsy and slow. Typically it needs to handle array of of size thousands to tens of thousands. I wonder how would the venerable monks here would make it more efficient and compact.
#!/usr/bin/perl -w
use strict;
use Data::Dumper;


my @set = qw (AAAAAT ATCGAT TTTTTG GCCCCC GTGGGG);
my $lim = 0.75;
my @sel = remove_poly( \@set, $lim);

print "BEFORE:",scalar(@set),"\n";
print "AFTER:",scalar(@sel),"\n";
#print Dumper \@sel;

sub remove_poly
{
    my ($array,$lim) = @_;
    
    my $len = length $array->[0];
    my @sel_array;
    
    foreach  ( @{$array} )
    {
       my $a_count = $_ =~ tr/A//;
       my $t_count = $_ =~ tr/T//;
       my $c_count = $_ =~ tr/C//;
       my $g_count = $_ =~ tr/G//;


       my $a_portion = $a_count/$len;
       my $t_portion = $t_count/$len;
       my $c_portion = $c_count/$len;
       my $g_portion = $g_count/$len;

       #print "$_ $a_portion $t_portion $c_portion $g_portion \n";
             
       if ( $a_portion < $lim && $t_portion < $lim && $c_portion < $li
+m && $g_portion < $lim )
       {
           push @sel_array,$_;
       }
       else
       {
          print "$_\n";
          next; 
       }
       
    }               
    #print Dumper \@sel_array ;    
    return @sel_array;
}

[download]
Update: Benchmark
Thanks so much guys. It's been a great learning experience, as always. 
            Rate limbic    ewi  fang   roy auk1   brs_auk2 jdhed
limbic     4029/s     --  -58%  -64%  -67%  -76%      -77%  -85%
ewi        9693/s   141%    --  -14%  -21%  -42%      -45%  -64%
fang      11261/s   180%   16%    --   -8%  -32%      -37%  -58%
roy       12211/s   203%   26%    8%    --  -27%      -31%  -55%
auk1      16620/s   313%   71%   48%   36%    --       -6%  -38%
brs_auk2  17743/s   340%   83%   58%   45%    7%        --  -34%
jdhed     27022/s   571%  179%  140%  121%   63%       52%    --

[download]
Regards,
Edward

In reply to Removing Poly-ATCG from and Array of Strings by monkfan

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