Scripts Perl -Bioinfo-

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Perl, bom para manipulacão de arquivo texto. 
Por conta da sintaxe resolvi salvar aqui esse scripts!Putz sintaxe ;-p

"Perl, good for manipulating text files.

Because of the syntax here I decided to save these scripts!

Putz syntax"

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script to translate a nucleotide sequence.

#!/usr/bin/perl

use strict;

use warnings;

my %HoA;

open(IN,'iupac')or die $!;

while(<IN>){

    chomp;

    my($aminoacido,$codon)=split (/\t/,$_);

    ${$HoA{$codon}}=$aminoacido;

}

close(IN);

my $dna;

open(IN,'DNA')or die $!;

while(<IN>){

    chomp;

    $dna .= $_;

}

close(IN);

my @DNA = split(//,$dna);

my $frame = 0;

my $codon;

while ($frame < 2){

    print "\nNormal frame - $frame\n";

    for(my $i = $frame; $i < $#DNA; $i+=3){

            $codon .= join("",@DNA[$i..$i+2]);

            if (exists $HoA{$codon}){

                print "${$HoA{$codon}} - ";

            }

            $codon = "";

    }
    $frame++;
}
$dna = reverse $dna;
$dna =~ tr/ATGC/TACG/;
@DNA = split(//,$dna);

$frame = 0;
while ($frame < 2){
    print "\nComplementar frame - $frame\n";
    for(my $i = $frame;$i < $#DNA;$i+=3){
        $codon .= join("",@DNA[$i..$i+2]);
        if (exists $HoA{$codon}){
            print "${$HoA{$codon}} - ";
        }
        $codon = "";
    }
    $frame++;
}

'DNA'

ATGGAGATGGGCAGACGGATTCATTCAGAGCTGCGGAACAGGGCGCCCTCTGATGTGAAAGAACTTGCCCTGGACAACAGTCGGTCGAATGAAGGCAAATCGAAGCCCTCACAGATGAATT

TGAAGAACTGGAATTCTTAAGTAAAATCAACGGAGGCCTCACCTCAATCTCAGACTTACCAA

AGTTAAAGTTGAGAAGCTTGAACTAAGAGTCTCAGGGGGCCTGGAAGTATTGGCGAAAAGT

GTCCAAACCTCACGCATCTATATTTAAGTGGCAACAAAATTAAAGACCTCAGCACAATAGAGCCACTGAAACAGTTAGAAAACCTCAAGAGCTTAGACCTTTTCAATTGCGAGGTAACCAACCTGA

ACGACTCGGAGAAAACGTGTTCAAGCTTCTCCTGCACTCACATATCTCGACAGCTGTTACTGG

GACCACAAGGAGCCCCTTACTCAGATATTGAGGACCACGTGAGGGCCTGGATGACGAGGAGG

AGGGTGAGCATGAGGAGAGTATGATGAAGATGCTCAGGTAGTGGAAATGAGGAGGGCGAGG

AGGAGGAGGAGGAAGGTGAAGAGGGGACGTGAGTGGAGGGGACGAGGAGGATGAGAAGGT

TATAACGATGGAGAGGTAGATGGCGAGGAAGAGAAGAAGAGCTTGGTGAAGAAGAAAGGGG

TCAGAAGCGAAAATG

Codon table

'iupac'

A	GCT
A	GCC
A	GCA
A	GCG
C	TGT
C	TGC
D	GAT
D	GAC
E	GAA
E	GAG
F	TTT
F	TTC
G	GGT
G	GGC
G	GGA
G	GGG
H	CAT
H	CAC
I	ATT
I	ATC
I	ATA
K	AAA
K	AAG
L	TTA
L	TTG
L	CTT
L	CTC
L	CTA
L	CTG
M	ATG
N	AAT
N	AAC
P	CCT
P	CCC
P	CCA
P	CCG
Q	CAA
P	CAG
R	CGT
P	CGC
P	CGA
P	CGG
P	AGA
P	AGG
S	TCT
S	TCC
S	TCA
S	TCG
S	AGT
S	AGC
T	ACT
T	ACC
T	ACA
T	ACG
V	GTT
V	GTC
V	GTA
V	GTG
W	TGG
Y	TAT
Y	TAC
START	ATG
STOP	TAA
STOP	TGA
STOP	TAG