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

    elsif ( $cnt == 2 ) {
        $return_pos = $sames[0];
    }

    return ( $cnt, $return_pos );
}

sub translate {
    my $self  = shift;
    my $seq   = shift;
    my $frame = shift;

    # check $frame
    if ( defined $frame ) {
        if ( List::MoreUtils::PP::none { $_ == $frame } ( 0 .. 2 ) ) {
            confess Dump( { frame => $frame } ), "Wrong frame\n";
        }
    }
    else {
        $frame = 0;
    }

    if ( $frame != 0 ) {
        $seq = substr( $seq, $frame );    # delete first $frame bases from $seq
    }
    my $offset = length($seq) - ( length($seq) % 3 );
    substr( $seq, $offset, length($seq), '' );    # now $seq is 3n bp

    my $peptide    = "";
    my $codon2aa   = $self->codon2aa;
    my $codon_size = 3;
    for ( my $i = 0; $i < ( length($seq) - ( $codon_size - 1 ) ); $i += $codon_size ) {
        my $triplet = substr( $seq, $i, $codon_size );
        if ( exists $codon2aa->{$triplet} ) {

t/04.syn_nsy.t  view on Meta::CPAN

        = ( [ 0, 1 ], [ 1, 0 ], [ 0.5, 1.5 ], [ 0.5, 1.5 ], [ 0.75, 2.25 ], );

    for my $i ( 0 .. $#compare ) {
        my ( $exp1, $exp2 ) = @{ $expect[$i] };
        my ( $syn,  $nsy )  = $codon->comp_codons( @{ $compare[$i] } );
        is( $syn, $exp1, "syn $i" );
        is( $nsy, $exp2, "nsy $i" );
    }
}

{    # compare normal codons with frames
    my $codon = AlignDB::Codon->new( table_id => 1 );

    my @compare = (
        [qw{ TTT TTA 2 }], [qw{ TTT TTA 0 }], [qw{ TTT TTC 2 }], [qw{ TTT TTC 1 }],
        [qw{ TTT GTA 0 }], [qw{ TTT GTA 1 }], [qw{ TTT GTA 2 }], [qw{ TTG AGA 0 }],
        [qw{ TTG AGA 1 }], [qw{ TTG AGA 2 }],
    );

    my @expect = (
        [ 0,    1 ],

t/05.seq.t  view on Meta::CPAN

my $codon = AlignDB::Codon->new( table_id => 1 );

my $dna = "CGACGTCTTCGTACGGGACTAGCTCGTGTCGGTCGC";
my $pep = "RRLRTGLARVGR";

is( $codon->translate($dna), $pep, "translate full" );
is( $codon->translate( substr( $dna, 0, length($dna) - 1 ) ),
    substr( $pep, 0, length($pep) - 1 ), "translate minus one" );

eval { $codon->translate( $dna, -1 ); };
like( $@, qr{Wrong frame}i, "Wrong frame" );

done_testing();