Re: Need help with code

[grondilu]

in reply to Need help with code

You should use the 'g' regex modifier imho (see perlretut).

#!/usr/bin/perl -w
use strict;
use warnings;
use feature qw(say);

use constant GENETIC_CODE => {
    TCA => 'S', # Serine
    TCC => 'S', # Serine
    TCG => 'S', # Serine
    TCT => 'S', # Serine
    TTC => 'F', # Phenylalanine
    TTT => 'F', # Phenylalanine
    TTA => 'L', # Leucine
    TTG => 'L', # Leucine
    TAC => 'Y', # Tyrosine
    TAT => 'Y', # Tyrosine
    TAA => '_', # exit
    TAG => '_', # exit
    TGC => 'C', # Cysteine
    TGT => 'C', # Cysteine
    TGA => '_', # exit
    TGG => 'W', # Tryptophan
    CTA => 'L', # Leucine
    CTC => 'L', # Leucine
    CTG => 'L', # Leucine
    CTT => 'L', # Leucine
    GTT => 'V', # Valine
    GTC => 'V', # Valine
    GTA => 'V', # Valine
    GTG => 'V', # Valine
    GCT => 'A', # Alanine
    GCC => 'A', # Alanine
    GCA => 'A', # Alanine
    GCG => 'A', # Alanine
    GAT => 'D', # Aspartic Acid
    GAC => 'D', # Aspartic Acid
    GAA => 'E', # Glutamate
    GAG => 'E', # Glutamate
    GGT => 'G', # Glycine
    GGC => 'G', # Glycine
    GGA => 'G', # Glycine
    GGG => 'G', # Glycine
    CCA => 'P', # Phenylalanine
    CCC => 'P', # Phenylalanine
    CCG => 'P', # Phenylalanine
    CCT => 'P', # Phenylalanine
    CAC => 'H', # Histidine
    CAT => 'H', # Histidine
    CAA => 'Q', # Glutamine
    CAG => 'Q', # Glutamine
    CGA => 'R', # Arginine
    CGC => 'R', # Arginine
    CGG => 'R', # Arginine
    CGT => 'R', # Arginine
    ATA => 'I', # Isoleucine
    ATC => 'I', # Isoleucine
    ATT => 'I', # Isoleucine
    ATG => 'M', # Methionine
    ACA => 'T', # Threonine
    ACC => 'T', # Threonine
    ACG => 'T', # Threonine
    ACT => 'T', # Threonine
    AAC => 'N', # Asparagine
    AAT => 'N', # Asparagine
    AAA => 'K', # Lysine
    AAG => 'K', # Lysine
    AGC => 'S', # Serine
    AGT => 'S', # Serine
    AGA => 'R', # Arginine
    AGG => 'R', # Arginine
};

my $s = 'AGCCATGTAGCTAACTCAGGTTACATGGGGATGACCCCGCGACTTGGATTAGAGTCTCTTT
+TGGAATAAGCCTGAATGATCCGAGTAGCATCTCAG';

for ($s =~ /ATG (?:[ACGT]{3})*? (?: TAA | TAG | TGA )/gx) {
    my @codons = /[ACGT]{3}/g;
    say join '', map GENETIC_CODE->{$_}, @codons;
}

This gives me the following output:

M_
MGMTPRLGLESLLE_

PS. Thanks anyway for telling us about this site, it's pretty cool. It's kind like a game, except that you're doing some actual scientific work.

I solved the problem with some perl6 code:

use v6;
constant DNA-codon = Hash.new: <
    TTT F      CTT L      ATT I      GTT V
    TTC F      CTC L      ATC I      GTC V
    TTA L      CTA L      ATA I      GTA V
    TTG L      CTG L      ATG M      GTG V
    TCT S      CCT P      ACT T      GCT A
    TCC S      CCC P      ACC T      GCC A
    TCA S      CCA P      ACA T      GCA A
    TCG S      CCG P      ACG T      GCG A
    TAT Y      CAT H      AAT N      GAT D
    TAC Y      CAC H      AAC N      GAC D
    TAA Stop   CAA Q      AAA K      GAA E
    TAG Stop   CAG Q      AAG K      GAG E
    TGT C      CGT R      AGT S      GGT G
    TGC C      CGC R      AGC S      GGC G
    TGA Stop   CGA R      AGA R      GGA G
    TGG W      CGG R      AGG R      GGG G 
>;
sub revc($dna) {
    $dna.comb.reverse.join.trans:
    [<A C T G>] => [<T G A C>]
}

sub orf($dna) {
    my %match;
    my @match = gather for $dna, revc $dna {
    take .match: rx/ ATG [ <[ACGT]>**3 ]*? <before TAA|TAG|TGA> /, :ov
+erlap;
    };
    %match{
    [~] map { DNA-codon{$_} }, .match: rx/ <[ACGT]>**3 /, :g
    }++ for @match;
    return %match.keys;
}

.say for orf open('rosalind_orf.txt').get;

The "overlap" option was much useful.