Beefy Boxes and Bandwidth Generously Provided by pair Networks
Keep It Simple, Stupid

Re: DNA Reverse Complement

by jkahn (Friar)
on Sep 14, 2002 at 05:12 UTC ( #197795=note: print w/ replies, xml ) Need Help??

in reply to DNA Reverse Complement

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?

Comment on Re: DNA Reverse Complement
Select or Download Code
Replies are listed 'Best First'.
Re^2: DNA Reverse Complement
by Aristotle (Chancellor) on Sep 14, 2002 at 05:36 UTC
    sub revcompl { return map { (my $rev = reverse $_) =~ tr/ACGTacgt/TGCAtgca/; $rev + } @_ }

    Makeshifts last the longest.

      The above sub does not work

        Of course it does. I'm guessing you called it in scalar context and got the count of the transform; e.g., 1.

        print revcompl("CGTAGTC"), $/; # GACTACG print scalar revcompl("CGTAGTC"), $/; # 1

        There was just a post on this issue this morning: Mini-Tutorial: Scalar vs List Assignment Operator.

Log In?

What's my password?
Create A New User
Node Status?
node history
Node Type: note [id://197795]
and the web crawler heard nothing...

How do I use this? | Other CB clients
Other Users?
Others contemplating the Monastery: (7)
As of 2015-11-30 00:04 GMT
Find Nodes?
    Voting Booth?

    What would be the most significant thing to happen if a rope (or wire) tied the Earth and the Moon together?

    Results (754 votes), past polls