Bio::Map::GenePositionUser Contributed Perl DocumentaBio::Map::GenePosition(3)NAMEBio::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).
perl v5.14.1 2011-07-22 Bio::Map::GenePosition(3)
