Beefy Boxes and Bandwidth Generously Provided by pair Networks
P is for Practical
 
PerlMonks  

Re: DNA Reverse Complement

by jkahn (Friar)
on Sep 14, 2002 at 05:12 UTC ( [id://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?

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?
Username:
Password:

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

How do I use this?Last hourOther CB clients
Other Users?
Others about the Monastery: (4)
As of 2024-04-19 22:56 GMT
Sections?
Information?
Find Nodes?
Leftovers?
    Voting Booth?

    No recent polls found