use Bio::SeqIO;

my $sequences = Bio::SeqIO->new( 
    -file   => "sequence.fasta",
    -format => "fasta",
);

while ( my $dna = $sequences->next_seq ){
    my $protein = $dna->translate( 
        -codontable_id => 1, # standard genetic code
        -frame         => 0, #reading-frame offset 0
    );
    print $dna->display_id, "\n";
    print $protein->seq, "\n\n";
}
[download]

#!/usr/bin/perl
use warnings;
use strict;


print 'ENTER THE FILENAME OF THE DNA SEQUENCE:= ';
chomp( my $DNAfilename = <STDIN> );

open my $DNAFILE, $DNAfilename or die qq[Cannot open file "$DNAfilenam
+e" because: $!];

local $/;
( my $DNA = uc <$DNAFILE> ) =~ tr/ACGT//cd;

print "\nThe original DNA file is:\n$DNA\n";

my %codon2aa = qw(
    TCA  S  TCC  S  TCG  S  TCT  S  TTC  F  TTT  F  TTA  L  TTG  L
    TAC  Y  TAT  Y  TAA  _  TAG  _  TGC  C  TGT  C  TGA  _  TGG  W
    CTA  L  CTC  L  CTG  L  CTT  L  CCA  P  CCC  P  CCG  P  CCT  P
    CAC  H  CAT  H  CAA  Q  CAG  Q  CGA  R  CGC  R  CGG  R  CGT  R
    ATA  I  ATC  I  ATT  I  ATG  M  ACA  T  ACC  T  ACG  T  ACT  T
    AAC  N  AAT  N  AAA  K  AAG  K  AGC  S  AGT  S  AGA  R  AGG  R
    GTA  V  GTC  V  GTG  V  GTT  V  GCA  A  GCC  A  GCG  A  GCT  A
    GAC  D  GAT  D  GAA  E  GAG  E  GGA  G  GGC  G  GGG  G  GGT  G
    );

my $protein = '';
while ( $DNA =~ /(...)/g ) {
    exists $codon2aa{ $1 } or die qq[Bad codon "$1"!!\n];
    $protein .= $codon2aa{ $1 };
    }

print "The translated protein is :\n$protein\n";
<STDIN>;
[download]

What is this, a question or a code submission? If you're not asking a question then you've posted it in the wrong place. A link to Where should I post X? is displayed each time you post. Seekers of Perl Wisdom is for questions, Cool Uses for Perl is for code you want to share.

You may want to read open, use the 3 argument open and actually die if you can't open your input file, printing $! to tell users why it fails.

G'day yuvraj_ghaly,

"This code will help to translate a DNA sequence to protein sequence. The need of an our is to translate all the DNA sequences present in fasta file into protein sequences respectively. Here is the code: ..."

There is no question here!

You have been directed to "How do I post a question effectively?" on more than one occasion in the past. Please actually read it this time and follow its guidelines.

I have downvoted your post.

The OP is looking for help with a FASTA parser; the 'question' was just worded as a statement of what they need.

Bioinformatics

"Here is the code:"

What is the question?

The question is I would like to extract sequences from multi-fasta file. How would I modify this code to do so

Now I created a modified program for translating DNA sequences.

It seems to give error output:

"Bad Codon ATGATCTAGTCGATCGCTAGCTAGATCGCTAGCTGC......!!!!"

I want to translate DNA sequences that are present in fasta file into their respective sequences. I need help from Perl monks.

Here is the code which I used now

use strict;
#use warnings;
use Encode; 

for my $file (@ARGV) {
    open my $fh, '<:encoding(UTF-8)', $file;
    my $input = join q{}, <$fh>; 
    close $fh;
   
   while ( $input =~ /(^>.*?\w?)$([^>]*)/smxg ) {
   
        my $name = $1;
        my $seq = $2;
        $seq =~ s/\n//smxg;
        my $trans = codon2aa($seq);
        print "$name\t$trans\n";
    }
}

sub codon2aa {
    my($codon) = @_;

    $codon = uc $codon;
 
    my(%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' => '_',    # Stop
    'TAG' => '_',    # Stop
    'TGC' => 'C',    # Cysteine
    'TGT' => 'C',    # Cysteine
    'TGA' => '_',    # Stop
    'TGG' => 'W',    # Tryptophan
    'CTA' => 'L',    # Leucine
    'CTC' => 'L',    # Leucine
    'CTG' => 'L',    # Leucine
    'CTT' => 'L',    # Leucine
    'CCA' => 'P',    # Proline
    'CCC' => 'P',    # Proline
    'CCG' => 'P',    # Proline
    'CCT' => 'P',    # Proline
    '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
    'GTA' => 'V',    # Valine
    'GTC' => 'V',    # Valine
    'GTG' => 'V',    # Valine
    'GTT' => 'V',    # Valine
    'GCA' => 'A',    # Alanine
    'GCC' => 'A',    # Alanine
    'GCG' => 'A',    # Alanine
    'GCT' => 'A',    # Alanine
    'GAC' => 'D',    # Aspartic Acid
    'GAT' => 'D',    # Aspartic Acid
    'GAA' => 'E',    # Glutamic Acid
    'GAG' => 'E',    # Glutamic Acid
    'GGA' => 'G',    # Glycine
    'GGC' => 'G',    # Glycine
    'GGG' => 'G',    # Glycine
    'GGT' => 'G',    # Glycine
    );

    if(exists $genetic_code{$codon}) {
        return $genetic_code{$codon};
    }else{

            print STDERR "Bad codon \"$codon\"!!\n";
            exit;
    }
}
[download]

The subroutine is called "codon2aa". You supply the sequence as the parameter, but you should run it on individual codons:

    for my $codon ($seq =~ /(...)/g) {
        my $trans = codon2aa($codon);
        print "$name\t$trans\n";
    }
[download]

لսႽ† ᥲᥒ⚪⟊Ⴙᘓᖇ Ꮅᘓᖇ⎱ Ⴙᥲ𝇋ƙᘓᖇ

This won't work when numerous DNA sequences in fasta file