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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
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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

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