NAME

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

SYNOPSIS

use Bio::Map::GeneRelative;

# say that a somthing 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())

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq