Bio::Map::GenePosition.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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).