Hi

Not as polished as the example above, but outputs the same results

use strict;
use warnings;

my @processed;
while (my $a_line = <DATA>) {
    chomp $a_line;
    if ($a_line =~ /^>/) {
        #this is a header, keep as is
        push @processed, $a_line;
    }
    else {
        # This is a dna seq, process
        #' Translate each three-base codon into amino acid, 
        # and append to a protein
        my $protein = '';
        my $len = length($a_line) -2;
           for(my $i=0; $i < $len ; $i += 3)
        {
           my $codon = substr($a_line, $i,3);
              $protein .= codon2aa($codon);
        }
        push @processed, $protein;
    }
}

#now display what we have processed
print $_, "\n" for @processed;


#' codon2aa
#'
#' A subroutine to translate a DNA 3-character codon to an amino acid

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

       if ( $codon =~ /GC./i)        { return 'A' }    # Alanine
    elsif ( $codon =~ /TG[TC]/i)    { return 'C' }    # Cysteine
    elsif ( $codon =~ /GA[TC]/i)    { return 'D' }    # Aspartic Acid
    elsif ( $codon =~ /GA[AG]/i)    { return 'E' }    # Glutamic Acid
    elsif ( $codon =~ /TT[TC]/i)    { return 'F' }    # Phenylalanine
    elsif ( $codon =~ /GG./i)        { return 'G' }    # Glycine
    elsif ( $codon =~ /CA[TC]/i)    { return 'H' }    # Histidine
    elsif ( $codon =~ /AT[TCA]/i)    { return 'I' }    # Isoleucine
    elsif ( $codon =~ /AA[AG]/i)    { return 'K' }    # Lysine
    elsif ( $codon =~ /TT[AG]|CT./i)    { return 'L' }    # Leucine
    elsif ( $codon =~ /ATG/i)        { return 'M' }    # Methionine
    elsif ( $codon =~ /AA[TC]/i)    { return 'N' }    # Asparagine
    elsif ( $codon =~ /CC./i)        { return 'P' }    # Proline
    elsif ( $codon =~ /CA[AG]/i)    { return 'Q' }    # Glutamine
    elsif ( $codon =~ /CG.|AG[AG]/i)    { return 'R' }    # Arginine
    elsif ( $codon =~ /TC.|AG[TC]/i)    { return 'S' }    # Serine
    elsif ( $codon =~ /AC./i)        { return 'T' }    # Threonine
    elsif ( $codon =~ /GT./i)        { return 'V' }    # Valine
    elsif ( $codon =~ /TGG/i)        { return 'W' }    # Tryptophan
    elsif ( $codon =~ /TA[TC]/i)    { return 'Y' }    # Tyrosine
    elsif ( $codon =~ /TA[AG]|TGA/i)    { return '_' }    # Stop
    else {
    return '*';
    }
}


__DATA__
>M01096:4:000000000-A23M1:1:1101:15974:1529 1:N:0:16
GTTACTGAGTGTGGTTGGCAGACTGCTGGTTGCCGTATGTAT
>M01096:4:000000000-A23M1:1:1101:16525:1548 1:N:0:16
CTTTCTCATTGTGATGTTAAGGATTGGATGTGCTGGCTTCTG
>M01096:4:000000000-A23M1:1:1101:13838:1554 1:N:0:16
GCTTGGACTTGTGTTGAGATTGATGGTCATTTCTCTATGAAT


[download]

Output

>M01096:4:000000000-A23M1:1:1101:15974:1529 1:N:0:16
VTECGWQTAGCRMY
>M01096:4:000000000-A23M1:1:1101:16525:1548 1:N:0:16
LSHCDVKDWMCWLL
>M01096:4:000000000-A23M1:1:1101:13838:1554 1:N:0:16
AWTCVEIDGHFSMN

[download]

Arnaud