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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";

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

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