NAME

Bio::Map::GenePosition - A typed position, suitable for modelling the various regions of a gene.

SYNOPSIS

    use Bio::Map::GenePosition;
    use Bio::Map::GeneMap;

    # say that the first transcript of a particular gene on a particular map
    # (species) is 1000bp long
    my $map = Bio::Map:GeneMap->get(-universal_name => 'BRCA2',
                                    -species => 'human');
    my $gene = $map->gene;
    Bio::Map::GenePosition->new(-map => $map, 
                                -element => $gene,
                                -start => 0,
                                -length => 1000,
                                -type => 'transcript');

    # say that the coding region of the gene starts 30bp into the first
    # transcript
    Bio::Map::GenePosition->new(-map => $map, 
                                -element => $gene,
                                -start => 30,
                                -length => 600,
                                -type => 'coding');

    # A GenePosition isa PositionWithSequence, so can have sequence associated
    # with it
    my $exon = Bio::Map::GenePosition->new(-map => $map, 
                                -element => $gene,
                                -start => 0,
                                -type => 'exon',
                                -seq => 'ATGGGGTGGG');
    my $length = $exon->length; # $length is 10

DESCRIPTION

Define where various sub-regions (transcripts, exons, introns etc.) of a gene are. Do this so that you can then go onto to model other mappable elements as having positions 20bp upstream of transcript 2, or 10bp into intron 3 etc., all without having to know the absolute position of anything.

See Bio::Map::GeneRelative and t/Map/Map.t for more example usage.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

  http://bugzilla.open-bio.org/

AUTHOR - Sendu Bala

Email bix@sendu.me.uk

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

 Title   : new
 Usage   : my $obj = Bio::Map::GenePosition->new();
 Function: Builds a new Bio::Map::GenePosition object 
 Returns : Bio::Map::GenePosition
 Args    : -map      => Bio::Map::GeneMap object
           -element  => Bio::Map::Gene object
           -relative => Bio::Map::GeneRelative object
           -type     => 'transcript|coding|exon|intron', REQUIRED
           -seq      => string, length of this string will set the length
                        of this position's range

           * If this position has no range, or if a single value can describe
             the range *
           -value => scalar             : something that describes the single
                                          point position or range of this
                                          Position, most likely an int

           * Or if this position has a range, at least two of *
           -start => int                : value of the start co-ordinate
           -end => int                  : value of the end co-ordinate
           -length => int               : length of the range

map

 Title   : map
 Usage   : my $map = $position->map();
           $position->map($map);
 Function: Get/set the map the position is in.
 Returns : L<Bio::Map::MapI>
 Args    : none to get
           new L<Bio::Map::MapI> to set

element

 Title   : element
 Usage   : my $element = $position->element();
           $position->element($element);
 Function: Get/set the element the position is for.
 Returns : L<Bio::Map::MappableI>
 Args    : none to get
           new L<Bio::Map::MappableI> to set

type

 Title   : type
 Usage   : my $type = $position->type();
           $position->type($type);
 Function: Get/set the type of this position.
 Returns : string
 Args    : none to get, OR
           string transcript|coding|exon|intron to set

relative

  Title   : relative
  Usage   : my $relative = $position->relative();
            $position->relative($relative);
  Function: Get/set the thing this Position's coordinates (numerical(), start(),
            end()) are relative to, as described by a RelativeI object.
  Returns : Bio::Map::GeneRelative. The default GeneRelative returned has a
            meaning that depends on the type() of GenePosition this is:
            'transcript'         : "relative to the start of the gene on the
                                    Position's map"
            'coding|exon|intron' : "relative to the start of the default
                                    transcript of the gene on the Position's map"
  Args    : none to get, OR
            Bio::Map::GeneRelative to set

seq

 Title   : seq
 Usage   : my $string = $position->seq();
 Function: Get/set the sequence as a string of letters. If no sequence is
           manually set by you, the position's map will be asked for the
           sequence, and if available, that will be returned.
 Returns : scalar
 Args    : Optionally on set the new value (a string). An optional second
           argument presets the alphabet (otherwise it will be guessed).