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Bio-Translator-v0.6.1
River stage zero No dependents
++
/ Bio::Translator::Table

NAME

Bio::Translator::Table - translation table

SYNOPSIS

    use Bio::Translator::Table;
    
    my $table = new Bio::Translator();
    my $table = new Bio::Translator(11);
    my $table = new Bio::Translator( 12, { type => 'id' } );
    my $table = new Bio::Translator( 'Yeast Mitochondrial', { type => 'name' } );
    my $table = new Bio::Translator( 'mito', { type => 'name' } );

    my $table = custom Bio::Translator( \$custom_table );
    my $tale = custom Bio::Translator( \$custom_table, { bootstrap => 0 } );

CONSTRUCTORS

new

    my $table = Bio::Translator::Table->new();
    my $table = Bio::Translator::Table->new( $id );
    my $table = Bio::Translator::Table->new( $id, \%params );

This method creates a translation table by loading a table string from the internal list. Pass an ID and the type of ID. By default, it will load the translation table with id 1. The type of ID may be "id" or "name," which correspond to the numeric id of the translation table or the long name of the translation table. For instance, below are the headers for the first 3 table strings.

    {
    name "Standard" ,
    name "SGC0" ,
    id 1 ,
    ...
    },
    {
    name "Vertebrate Mitochondrial" ,
    name "SGC1" ,
    id 2 ,
    ...
    },
    {
    name "Yeast Mitochondrial" ,
    name "SGC2" ,
    id 3 ,
    ...
    },
    ...

By default, the "Standard" translation table will be loaded. You may instantiate this translation table by calling any of the following:

    my $t = Bio::Translator::Table->new();
    my $t = Bio::Translator::Table->new(1);
    my $t = Bio::Translator::Table->new( 1,          { type => 'id' } );
    my $t = Bio::Translator::Table->new( 'Standard', { type => 'name' } );
    my $t = Bio::Translator::Table->new( 'SGC0',     { type => 'name' } );
    my $t = Bio::Translator::Table->new( 'standard', { type => 'name' } );
    my $t = Bio::Translator::Table->new( 'stan',     { type => 'name' } );

For partial matches, this module will use the first matching translation table.

    my $t = Bio::Translator::Table->new( 'mitochondrial', { type => 'name' } );

This will use translation table with ID 2, "Vertebrate Mitochondrial," because that is the first match (even though "Yeast Mitochondrial" would also match).

custom()

    my $table = Bio::Translator::Table->custom( $table_ref );
    my $table = Bio::Translator::Table->custom( $table_ref, \%params );

Create a translation table based off a passed table reference for custom translation tables. Loads degenerate nucleotides if bootstrap isn't set (this can take a little time). The format of the translation table should reflect those of the internal tables:

    name "Names separated; by semicolons"
    name "May have multiple lines"
    id 99
    ncbieaa  "AMINOACIDS...",
    sncbieaa "-M--------..."
    -- Base1  AAAAAAAAAA...
    -- Base2  AAAACCCCGG...
    -- Base3  ACGTACTGAC...

Examples:

    $translator = new Translator(
        table_ref => \'name "All Alanines; All the Time"
                       id 9000
                       ncbieaa  "AAAAAAAA"
                       sncbieaa "----M---"
                       base1     AAAAAAAA
                       base2     AACCGGTT
                       base3     ACACACAC'
    );

    $translator = new Translator(
        table_ref => \$table,
        bootstrap  => 0
    );

METHODS

add_translation

    $translator->add_translation( $codon, $residue );
    $translator->add_translation( $codon, $residue, \%params );

Add a codon-to-residue translation to the translation table. $start inidicates if this is a start codon.

Examples:

    # THESE AREN'T REAL!!!
    $translator->add_translation( 'ABA', 'G' );
    $translator->add_translation( 'ABA', 'M', { start => 1, strand => -1 } );

bootstrap

    $translator->bootstrap();

Bootstrap the translation table. Find every possible translation, even those that involve degenerate nucleotides or ambiguous amino acids.

string

    my $table_string_ref = $translator->string();
    my $table_string_ref = $translator->string( \%params );

Returns the table string. %params can specify whether or not this table should try to bootstrap itself using the bootstrap function above. By default, it will try to.

Examples:

    my $table_string_ref = $translator->string();
    my $table_string_ref = $translator->string( { bootstrap => 0 } );

MISC

These are the original translation tables. The translation tables used by this module have been boostrapped and compacted. They were first expanded to include translations for degenerate nucleotides and allow ambiguous amino acids to be the targets of translation (e.g. every effort has been made to give a translation that isn't "X"). Then, the tables had reduntant columns removed; any codon implied by the presence of degenerate-nucleotide-containing codon was removed.

    {
    name "Standard" ,
    name "SGC0" ,
    id 1 ,
    ncbieaa  "FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
    sncbieaa "---M---------------M---------------M----------------------------"
    -- Base1  TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
    -- Base2  TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
    -- Base3  TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
    },
    {
    name "Vertebrate Mitochondrial" ,
    name "SGC1" ,
    id 2 ,
    ncbieaa  "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG",
    sncbieaa "--------------------------------MMMM---------------M------------"
    -- Base1  TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
    -- Base2  TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
    -- Base3  TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
    },
    {
    name "Yeast Mitochondrial" ,
    name "SGC2" ,
    id 3 ,
    ncbieaa  "FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
    sncbieaa "----------------------------------MM----------------------------"
    -- Base1  TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
    -- Base2  TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
    -- Base3  TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
    },
    {
    name "Mold Mitochondrial; Protozoan Mitochondrial;"
    name "Coelenterate Mitochondrial; Mycoplasma; Spiroplasma" ,
    name "SGC3" ,
    id 4 ,
    ncbieaa  "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
    sncbieaa "--MM---------------M------------MMMM---------------M------------"
    -- Base1  TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
    -- Base2  TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
    -- Base3  TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
    },
    {
    name "Invertebrate Mitochondrial" ,
    name "SGC4" ,
    id 5 ,
    ncbieaa  "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG",
    sncbieaa "---M----------------------------MMMM---------------M------------"
    -- Base1  TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
    -- Base2  TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
    -- Base3  TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
    },
    {
    name "Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear" ,
    name "SGC5" ,
    id 6 ,
    ncbieaa  "FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
    sncbieaa "-----------------------------------M----------------------------"
    -- Base1  TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
    -- Base2  TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
    -- Base3  TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
    },
    {
    name "Echinoderm Mitochondrial; Flatworm Mitochondrial" ,
    name "SGC8" ,
    id 9 ,
    ncbieaa  "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG",
    sncbieaa "-----------------------------------M---------------M------------"
    -- Base1  TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
    -- Base2  TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
    -- Base3  TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
    },
    {
    name "Euplotid Nuclear" ,
    name "SGC9" ,
    id 10 ,
    ncbieaa  "FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
    sncbieaa "-----------------------------------M----------------------------"
    -- Base1  TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
    -- Base2  TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
    -- Base3  TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
    },
    {
    name "Bacterial and Plant Plastid" ,
    id 11 ,
    ncbieaa  "FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
    sncbieaa "---M---------------M------------MMMM---------------M------------"
    -- Base1  TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
    -- Base2  TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
    -- Base3  TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
    },
    {
    name "Alternative Yeast Nuclear" ,
    id 12 ,
    ncbieaa  "FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
    sncbieaa "-------------------M---------------M----------------------------"
    -- Base1  TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
    -- Base2  TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
    -- Base3  TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
    },
    {
    name "Ascidian Mitochondrial" ,
    id 13 ,
    ncbieaa  "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG",
    sncbieaa "---M------------------------------MM---------------M------------"
    -- Base1  TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
    -- Base2  TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
    -- Base3  TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
    },
    {
    name "Alternative Flatworm Mitochondrial" ,
    id 14 ,
    ncbieaa  "FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG",
    sncbieaa "-----------------------------------M----------------------------"
    -- Base1  TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
    -- Base2  TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
    -- Base3  TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
    } ,
    {
    name "Blepharisma Macronuclear" ,
    id 15 ,
    ncbieaa  "FFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
    sncbieaa "-----------------------------------M----------------------------"
    -- Base1  TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
    -- Base2  TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
    -- Base3  TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
    } ,
    {
    name "Chlorophycean Mitochondrial" ,
    id 16 ,
    ncbieaa  "FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
    sncbieaa "-----------------------------------M----------------------------"
    -- Base1  TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
    -- Base2  TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
    -- Base3  TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
    } ,
    {
    name "Trematode Mitochondrial" ,
    id 21 ,
    ncbieaa  "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG",
    sncbieaa "-----------------------------------M---------------M------------"
    -- Base1  TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
    -- Base2  TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
    -- Base3  TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
    } ,
    {
    name "Scenedesmus obliquus Mitochondrial" ,
    id 22 ,
    ncbieaa  "FFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
    sncbieaa "-----------------------------------M----------------------------"
    -- Base1  TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
    -- Base2  TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
    -- Base3  TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
    } ,
    {
    name "Thraustochytrium Mitochondrial" ,
    id 23 ,
    ncbieaa  "FF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
    sncbieaa "--------------------------------M--M---------------M------------"
    -- Base1  TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
    -- Base2  TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
    -- Base3  TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
    }

AUTHOR

Kevin Galinsky, <kgalinsky plus cpan at gmail dot com>