| Bio::Map::GeneRelative(3pm) | User Contributed Perl Documentation | Bio::Map::GeneRelative(3pm) |
Bio::Map::GeneRelative - Represents being relative to named
sub-regions of a
gene.
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>
Be able to say that a given position is relative to some standard part of a gene.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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.
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
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
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.
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.
Title : exon
Usage : my ($exon_number, $transcript_number) = @{$relative->exon()};
$relative->exon($exon_number, $transcript_number);
Function: Get/set which exon of which transcript of the Position's map's gene
the Position's co-ordinates are relative to.
Returns : reference to list with two ints, exon number and transcript number
Args : none to get, OR
int (exon number) AND int (transcript number) to set. The second int
is optional and defaults to 0 (meaning default/active transcript).
Title : intron
Usage : my ($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).
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())
| 2018-10-27 | perl v5.26.2 |