Provided by: libbio-perl-perl_1.7.2-3_all bug


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


           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


       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.


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AUTHOR - Sendu Bala



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

        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

        Title   : map
        Usage   : my $map = $position->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

        Title   : element
        Usage   : my $element = $position->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

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

         Title   : relative
         Usage   : my $relative = $position->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

        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).