comment on

toolic expertly provided the solution to your script's concatenation issue. However, consider using Bio::SeqIO for your Fasta-parsing needs:

use strict;
use warnings;
use Bio::SeqIO;

my $in = Bio::SeqIO->new( -fh => \*ARGV, -format => 'Fasta' );

while ( my $seq = $in->next_seq() ) {
    my $protein;
    $protein .= codon2aa($_) for $seq->seq =~ /.../g;
    print '>' . $seq->id . "\n$protein\n";
}

#' 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 Aci
+d
    elsif ( $codon =~ /GA[AG]/i )     { return 'E' }    # Glutamic Aci
+d
    elsif ( $codon =~ /TT[TC]/i )     { return 'F' }    # Phenylalanin
+e
    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 '*';
    }
}
[download]

Output on your data set:

>M01096:4:000000000-A23M1:1:1101:15974:1529
VTECGWQTAGCRMY
>M01096:4:000000000-A23M1:1:1101:16525:1548
LSHCDVKDWMCWLL
>M01096:4:000000000-A23M1:1:1101:13838:1554
AWTCVEIDGHFSMN
[download]

In reply to Re: How do I stop appending data by Kenosis
in thread How do I stop appending data by 4pt8secs

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