Beefy Boxes and Bandwidth Generously Provided by pair Networks Cowboy Neal with Hat
Syntactic Confectionery Delight
 
PerlMonks  

Re: (Golf) Fragment Reassembly

by jepri (Parson)
on May 02, 2001 at 09:28 UTC ( #77245=note: print w/ replies, xml ) Need Help??


in reply to (Golf) Fragment Reassembly

Update: A while ago I saw an absolutely fantastic piece of art on film. It was only a minute or two long. The artist had done some visual thing, but the highlight for me was that he/she had a person reading words that were joined together, similar to what I did to MeowChows post below. It was always just on the edge of understandable. I think it was called 'Mouth Music'. Anyway, it rocked.

Well, here's code that does some of what you want. What I would really like to see is a mathematical proof of the minimum number and length of sequences to get complete reconstruction of the thing you chopped up in the first place.

Plus, when you golf, aren't you meant to post your own code for other people to play with? Maybe I should call homework on this :)

Here are the results:

logger,gerbil,log,analog, Constructed sequence is analoggerbil GATTACA,ATTACA,GATT,AAGAT,CCC, Constructed sequence is gattacaagatt Fragment,Reassembly,by,MeowChow,... Constructed sequence is byoureassemblesuperstringolfednakasubstringseq +uencing

And here is the code that did it:

use strict; sub assemble{ my @sequences = sort {length($b) <=> length($a)} @_; &text_mangle($_) for @sequences; my $a=shift @sequences; my $b=shift @sequences; while ( @sequences ) { my $c=overlap($a,$b); if ( defined($c) ) { $a=$c; #push @sequences,$b; $b=shift @sequences; } else { push @sequences,$b; $b=shift @sequences; } } print "Constructed sequence is $a\n"; }; sub overlap{ my ($a,$b)=@_; my ($i,$l); if ($a=~/ / || $b=~/ / ) { die "Don't use spaces in your data! +\n";} $l=length($a); for ($i=0;$i<$l; $i++ ) { if ( substr($a,$i,$l-$i) eq substr($b,0,$l-$i) ) { substr($a,$i,($l-$i))= $b; return $a; } } $l=length($b); for ($i=0;$i<$l; $i++ ) { if ( lc(substr($b,$i,$l-$i)) eq lc(substr($a,0,$l-$i)) + ) { substr($b,$i,($l-$i))= $a ; return $b; } return undef; }; sub text_mangle { $_[0]=~s/ |\.|\,//g; my $a=lc($_[0]); $_[0]=$a; } sub swap { my $a=$_[0]; $_[0]=$_[1]; $_[1]=$a; } my @array=qw(logger gerbil log analog); foreach (@array) {print; print ",";};print "\n";assemble(@array);print + "\n"; @array=qw(GATTACA ATTACA GATT AAGAT CCC); foreach (@array) {print; print ",";};print "\n";assemble(@array);print + "\n"; @array=qw(Fragment Reassembly by MeowChow ... aka DNA Sequencing or Shortest Common Superstring. Your mission, s +hould you choose to accept it, is to design a golfed sforeach (@array +) {print; print ",";};print "\n";assemble(@array);print "\n";

____________________
Jeremy
I didn't believe in evil until I dated it.


Comment on Re: (Golf) Fragment Reassembly
Select or Download Code

Log In?
Username:
Password:

What's my password?
Create A New User
Node Status?
node history
Node Type: note [id://77245]
help
Chatterbox?
and the web crawler heard nothing...

How do I use this? | Other CB clients
Other Users?
Others meditating upon the Monastery: (11)
As of 2014-04-18 14:09 GMT
Sections?
Information?
Find Nodes?
Leftovers?
    Voting Booth?

    April first is:







    Results (469 votes), past polls