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

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   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:

         https://github.com/bioperl/bioperl-live/issues

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).