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://redmine.open-bio.org/projects/bioperl/

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).

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq