Provided by: libbio-perl-perl_1.7.2-2_all bug

NAME

       Bio::Map::GeneRelative - Represents being relative to named sub-regions of a
                                gene.

SYNOPSIS

           use Bio::Map::GeneRelative;

           # say that a something will have a position relative to the start of the
           # gene on map
           my $rel = Bio::Map::GeneRelative->new(-gene => 0);

           # or that something will be relative to the third transcript of a gene
           # on a map
           $rel = Bio::Map::GeneRelative->new(-transcript => 3);

           # or to the 5th intron of the default transcript
           $rel = Bio::Map::GeneRelative->new(-intron => [0, 5]);

           # use the $rel as normal; see L<Bio::Map::Relative>

DESCRIPTION

       Be able to say that a given position is relative to some standard part of a gene.

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://github.com/bioperl/bioperl-live/issues

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 $relative = Bio::Map::Relative->new();
        Function: Build a new Bio::Map::Relative object.
        Returns : Bio::Map::Relative object
        Args    : -gene => int       : coordinates are relative to the int'th base
                                       downstream of the Position's map's gene
                                       [default is gene => 0, ie. relative to the
                                       start of the gene],
                  -transcript => int : or relative to the start of the int'th
                                       transcript of the Position's map's gene,
                  -exon => [i, n]    : or relative to the start of the n'th
                                       transcript's i'th exon,
                  -intron => [i, n]  : or intron,
                  -coding => int     : or the start of the int'th transcript's coding
                                       region.

                  -description => string : Free text description of what this relative
                                           describes

                  (To say a Position is relative to something and upstream of it,
                   the Position's start() co-ordinate should be set negative)
                  In all cases, a transcript number of 0 means the active transcript.

   absolute_conversion
        Title   : absolute_conversion
        Usage   : my $absolute_coord = $relative->absolute_conversion($pos);
        Function: Convert the start co-ordinate of the supplied position into a number
                  relative to the start of its map.
        Returns : scalar number
        Args    : Bio::Map::PositionI object

   type
        Title   : type
        Usage   : my $type = $relative->type();
        Function: Get the type of thing we are relative to. The types correspond
                  to a method name, so the value of what we are relative to can
                  subsequently be found by $value = $relative->$type;

                  Note that type is set by the last method that was set, or during
                  new().

        Returns : 'gene', 'transcript', 'exon', 'intron' or 'coding'
        Args    : none

   gene
        Title   : gene
        Usage   : my $int = $relative->gene();
                  $relative->gene($int);
        Function: Get/set the distance from the start of the gene that the Position's
                  co-ordiantes are relative to.
        Returns : int
        Args    : none to get, OR
                  int to set; a value of 0 means relative to the start of the gene.

   transcript
        Title   : transcript
        Usage   : my $int = $relative->transcript();
                  $relative->transcript($int);
        Function: Get/set which transcript of the Position's map's gene the Position's
                  co-ordinates are relative to.
        Returns : int
        Args    : none to get, OR
                  int to set; a value of 0 means the active (default) transcript.

   exon
        Title   : exon
        Usage   : my ($exon_number, $transcript_number) = @{$relative->exon()};
                  $relative->exon($exon_number, $transcript_number);
        Function: Get/set which exon of which transcript of the Position's map's gene
                  the Position's co-ordinates are relative to.
        Returns : reference to list with two ints, exon number and transcript number
        Args    : none to get, OR
                  int (exon number) AND int (transcript number) to set. The second int
                  is optional and defaults to 0 (meaning default/active transcript).

   intron
        Title   : intron
        Usage   : my ($intron_number, $transcript_number) = @{$relative->intron()};
                  $relative->intron($intron_number, $transcript_number);
        Function: Get/set which intron of which transcript of the Position's map's gene
                  the Position's co-ordinates are relative to.
        Returns : reference to list with two ints, intron number and transcript number
        Args    : none to get, OR
                  int (intron number) AND int (transcript number) to set. The second
                  int is optional and defaults to 0 (meaning default/active
                  transcript).

   coding
        Title   : coding
        Usage   : my $transcript_number = $relative->coding;
                  $relative->coding($transcript_number);
        Function: Get/set which transcript's coding region of the Position's map's gene
                  the Position's co-ordinates are relative to.
        Returns : int
        Args    : none to get, OR
                  int to set (the transcript number, see transcript())