The Genetic Code one-liner in Perl 6

masak on 2009-07-06T16:16:14

Today on #perl6:


<masak> rakudo: subset DNA of Str where { all(.uc.comb) eq any <A C G T> }; my DNA $dna = "gattaca"; say $dna;

<p6eval> rakudo 0e8a86: OUTPUTÃÂ«gattaca␤ÃÂ»

<jnthn> rakudo: subset DNA of Str where { all(.uc.comb) eq any <A C G T>}; my DNA $dna = "lolnotdna"; say $dna;

<p6eval> rakudo 0e8a86: OUTPUTÃÂ«Assignment type check failed [...]

<jnthn> (just checking :-))

<TimToady> course, where not /<-[ACGTactg]>/ might beat all those

<moritz_> but it involves no junction, so it can't be any good :-)

<TimToady> ttaggg &

<masak> halp, TimToady is speaking in DNA bases!

<masak> is my hunch right, and that actually means something as amino acids?

* masak checks

<pyrimidine> yes

<masak> TimToady++

<masak> rakudo: my $dna = "ttaagg"; sub translate($dna) { "FFLLSSSSYY!!CC!WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG".comb[map { :4($_) }, $dna.trans("tcag" => "0123").comb(/.../)] }; say translate($dna)

<p6eval> rakudo 0e8a86: OUTPUTÃÂ«LR␤ÃÂ»

<masak> that's what I got too.

<pyrimidine> masak: nice!

<masak> I know! :)

<masak> I should blog about it.

<masak> "The Genetic Code one-liner in Perl 6"

A hyper-short summary of what that one-liner does:

Convert each base into an integer. $dna.trans("tcag" => "0123")
Break up the DNA numbers in triplets. .comb(/.../)
Interpret each three-digit number as a quaternary integer between 0 and 63. map { :4($_) }
Use these numbers as indexes into an array of 64 one-character strings, each with the character of one amino acid.

Perl 6 feels more like a power tool every day.