Reverse complement

[bluray]

Hi Perlmonks,

Recently, I posted a question about creating a column of frequencies for the unique entries of other column (http://www.perlmonks.com/?node_id=934469). Thanks for the valuable inputs. In the same script, I did some tweaking to reverse complement the sequence under $1 and then print it like before. I am able to get the results, but I am curious if there is another neat way to do the step.

#!usr/bin/perl
use strict;
use warnings;

my $sequence='ABCD';
my @headings= qw/ Tags Frequency /;
my $headings=join("\t",@headings);
my @input_files=<*.seq>;

foreach my $input_file (@input_files)
{
    open INPUT, "<", $input_file or die "Cannot open file \"$input_fil
+e\". $!";
    (my $outfile = $input_file) =~ s/.seq/\.tag\.txt/i;
    my %freq;
    
    while (my $line=<INPUT>)
    {
        
        if ($line=~m/$sequence(.{11})(.{11})$sequence/i){
        my $revcomp=reverse($1);
        $revcomp=~tr/ACGTacgt/TGCAtgca/;

             $freq{$_}++ for $revcomp, $2;
           }
        
    }
    close INPUT or die "Cannot close file \"$input_file\". $!";
    open OUTPUT, ">", $outfile or die "Cannot open file \"$outfile\".
+ $!";
    
    print OUTPUT $headings, "\n";
    for my $tag (sort {$freq{$b} <=> $freq{$a}} keys %freq) {
            print OUTPUT $tag,"\t",$freq{$tag},"\n"; 
    }

    close OUTPUT or die "Unable to close \"$outfile\". $!";
}

[Marshall]

Hi bluray!

It looks to me like you paid attention to the suggestions in the previous post! I don't see anything glaring wrong here. If this does what you want functionally, I don't see a reason to keep tweaking. (well, I would spiff up the indenting) - but structurally, you have sound code.

If you are asking if

my $revcomp=reverse($1);
$revcomp=~tr/ACGTacgt/TGCAtgca/;

is fine, it is. reverse() is fast and tr is much faster than any other way to do a one->one character mapping. If you want to convert to all uppercase at the same time, $revcomp =~ tr/ACGTacgt/TGCATGCA/;