Bio::Map::GenePosition(3) A typed position, suitable for modelling the various


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

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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).