Beefy Boxes and Bandwidth Generously Provided by pair Networks
Your skill will accomplish
what the force of many cannot

DNA Reverse Complement

by mousey (Scribe)
on Sep 14, 2002 at 05:02 UTC ( #197793=snippet: print w/ replies, xml ) Need Help??

Description: A function to figure out the reverse complement of a DNA sequence
sub revdnacomp {
  my $dna = @_;
  my $revcomp = reverse($dna);

  $revcomp =~ tr/ACGTacgt/TGCAtgca/;

  return $revcomp;
Comment on DNA Reverse Complement
Download Code
Replies are listed 'Best First'.
Re: DNA Reverse Complement
by jkahn (Friar) on Sep 14, 2002 at 05:12 UTC
    I think you'll have a problem with the argument structure:
    sub revdnacomp { # my $dna = @_; # the above means $dna gets the number of # arguments in @_, since it's a scalar context! my $dna = shift; # or my $dna = shift @_; # ah, scalar context of scalar gives expected results. # my ($dna) = @_; # would work, too my $revcomp = reverse($dna); $revcomp =~ tr/ACGTacgt/TGCAtgca/; return $revcomp; }
    but why not allow the complementation over more than one element?
    sub revcompl { # operates on all elements passed in my (@dna) = @_; foreach my $segment (@dna) { my $revcomp = reverse($segment); $revcomp =~ tr/ACGTacgt/TGCAtgca/; push @done, $revcomp; } return @done; # or reverse @done; # what's best semantics? }
    Did I miss anything?
      sub revcompl { return map { (my $rev = reverse $_) =~ tr/ACGTacgt/TGCAtgca/; $rev + } @_ }

      Makeshifts last the longest.

        The above sub does not work

Back to Snippets Section

Log In?

What's my password?
Create A New User
Node Status?
node history
Node Type: snippet [id://197793]
and the web crawler heard nothing...

How do I use this? | Other CB clients
Other Users?
Others avoiding work at the Monastery: (4)
As of 2016-02-14 10:15 GMT
Find Nodes?
    Voting Booth?

    How many photographs, souvenirs, artworks, trophies or other decorative objects are displayed in your home?

    Results (470 votes), past polls