in reply to Removing Poly-ATCG from and Array of Strings


The following should does the same as yours... I don't know if it is faster... You could test this with the benchmark module: 
use strict;
use warnings;

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";

sub remove_poly
{
    my ($array,$lim) = @_;

    my $len = length $array->[0];
    my @sel_array;

    @sel_array = grep { ( ((tr/A//)/$len < $lim) &&
                          ((tr/T//)/$len < $lim) &&
                          ((tr/C//)/$len < $lim) &&
                          ((tr/G//)/$len < $lim)    ) and $_ } @$array
+;

    return @sel_array;
}

[download]
Now since this is a lot smaller, you could even take it out of the sub..

.:| If it can't be fixed .. Don't break it |:.

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Re^2: Removing Poly-ATCG from and Array of Strings
by aukjan (Friar) on Jun 09, 2005 at 12:59 UTC
    Another way is to use map on the original array and set all the entries which you don't want to '', and filter those out lateron.. 
    my @set = qw (AAAAAT ATCGAT TTTTTG GCCCCC GTGGGG);
my $lim = 0.75;
my $len = length $set[0];

print "BEFORE:",scalar(@set),"\n";

map  { ( ((tr/A//)/$len < $lim) &&
          ((tr/T//)/$len < $lim) &&
          ((tr/C//)/$len < $lim) &&
          ((tr/G//)/$len < $lim)    ) or $_ = '' } @set;

print "AFTER:",scalar(@set),"\n";

    [download]
    Now the @set contains:
    $VAR1 = '';
$VAR2 = 'ATCGAT';
$VAR3 = '';
$VAR4 = '';
$VAR5 = '';

    [download]

    .:| If it can't be fixed .. Don't break it |:.

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