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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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(); $position->map($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
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
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
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
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).