AlignDB-Codon

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lib/AlignDB/Codon.pm  view on Meta::CPAN

        'Vertebrate Mitochondrial',    # 2
        'Yeast Mitochondrial',         # 3
        'Mold, Protozoan, and Coelenterate Mitochondrial and Mycoplasma/Spiroplasma',    # 4
        'Invertebrate Mitochondrial',                                                    # 5
        'Ciliate, Dasycladacean and Hexamita Nuclear',                                   # 6
        '', '',
        'Echinoderm and Flatworm Mitochondrial',                                         # 9
        'Euplotid Nuclear',                                                              # 10
        'Bacterial, Archaeal and Plant Plastid',                                         # 11
        'Alternative Yeast Nuclear',                                                     # 12
        'Ascidian Mitochondrial',                                                        # 13
        'Alternative Flatworm Mitochondrial',                                            # 14
        'Blepharisma Nuclear',                                                           # 15
        'Chlorophycean Mitochondrial',                                                   # 16
        '', '', '', '',
        'Trematode Mitochondrial',                                                       # 21
        'Scenedesmus obliquus Mitochondrial',                                            # 22
        'Thraustochytrium Mitochondrial',                                                # 23
        'Pterobranchia Mitochondrial',                                                   # 24
        'Candidate Division SR1 and Gracilibacteria',                                    # 25
    );

lib/AlignDB/Codon.pm  view on Meta::CPAN

    }
}

sub _load_aa_code {
    my $self = shift;

    my %one2three = (
        A   => 'Ala',    # Alanine
        R   => 'Arg',    # Arginine
        N   => 'Asn',    # Asparagine
        D   => 'Asp',    # Aspartic acid
        C   => 'Cys',    # Cysteine
        Q   => 'Gln',    # Glutamine
        E   => 'Glu',    # Glutamic acid
        G   => 'Gly',    # Glycine
        H   => 'His',    # Histidine
        I   => 'Ile',    # Isoleucine
        L   => 'Leu',    # Leucine
        K   => 'Lys',    # Lysine
        M   => 'Met',    # Methionine
        F   => 'Phe',    # Phenylalanine
        P   => 'Pro',    # Proline
        S   => 'Ser',    # Serine
        T   => 'Thr',    # Threonine
        W   => 'Trp',    # Tryptophan
        Y   => 'Tyr',    # Tyrosine
        V   => 'Val',    # Valine
        B   => 'Asx',    # Aspartic acid or Asparagine
        Z   => 'Glx',    # Glutamine or Glutamic acid
        X   => 'Xaa',    # Any or unknown amino acid
        '*' => '***',    # Stop codon
    );
    my %three2one = reverse(%one2three);

    $self->{one2three} = \%one2three;
    $self->{three2one} = \%three2one;

    return;
}

lib/AlignDB/Codon.pm  view on Meta::CPAN

    $peptide = uc $peptide;
    my $three_of = $self->one2three;

    my $converted;
    for my $pos ( 0 .. length($peptide) - 1 ) {
        my $aa_code = substr( $peptide, $pos, 1 );
        if ( $three_of->{$aa_code} ) {
            $converted .= $three_of->{$aa_code};
        }
        else {
            Carp::confess "Wrong single-letter amino acid code [$aa_code]!\n";
            $converted .= ' ' x 3;
        }
    }
    return $converted;
}

sub convert_321 {
    my $self    = shift;
    my $peptide = shift;

lib/AlignDB/Codon.pm  view on Meta::CPAN

    my $one_of = $self->three2one;

    my $converted;
    for ( my $pos = 0; $pos < length($peptide); $pos += 3 ) {
        my $aa_code = substr( $peptide, $pos, 3 );
        $aa_code = ucfirst $aa_code;
        if ( $one_of->{$aa_code} ) {
            $converted .= $one_of->{$aa_code};
        }
        else {
            warn "Wrong three-letter amino acid code [$aa_code]!\n";
            $converted .= ' ' x 3;
        }

    }

    return $converted;
}

1;    # Magic true value required at end of module