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Laura Thomson on coding, the workplace, and FOSS
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Bio::Map::GeneRelative(3pm) User Contributed Perl Documentation Bio::Map::GeneRelative(3pm) 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://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 $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()) perl v5.14.2 2012-03-02 Bio::Map::GeneRelative(3pm)
