SYNOPSIS
use Bio::Map::Gene;
my $gene = Bio::Map::Gene->get(-universal_name => 'BRCA2',
-description => 'breast cancer 2, early onset');
# Normally you get Gene objects from GeneMaps
use Bio::Map::GeneMap;
# Model a gene with its orthologous versions found in different species,
# but at abstract locations within each genome
my $map1 = Bio::Map::GeneMap->get(-universal_name => 'BRCA2', -species => $human);
my $map2 = Bio::Map::GeneMap->get(-universal_name => 'BRCA2', -species => $mouse);
$gene = $map1->gene;
# Genes can have special kinds of positions (Bio::Map::GenePosition) that
# define where various sub-regions of the gene are, relative to one of the
# normal Positions the gene has placing it on a map.
my $trans = Bio::Map::GenePosition->new(-start => 0, -length => 700,
-map => $map1, -type => 'transcript');
$gene->add_transcript_position($trans);
my $exon = Bio::Map::GenePosition->new(-start => 0, -length => 100,
-map => $map1, -type => 'exon');
$gene->add_exon_position($exon, 1);
# (so now the gene has 1 transcript 700bp long which starts at the beginning
# of the gene, and we've defined the first of many exons which starts at the
# start of the transcript and is 100bp long)
DESCRIPTION
Model a gene as an abstract mappable element. This is for when you don't care exactly where a gene is in a genome, but just want to model other things (like transcription factor binding sites) that are near it so you can answer questions like ``what binds near this gene?'', or ``which genes does this bind near?''.See t/Map/Map.t for more example usage.
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AUTHOR - Sendu Bala
Email [email protected]APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _new
Title : new
Usage : my $gene = Bio::Map::Gene->new();
Function: Builds a new Bio::Map::Gene object
Returns : Bio::Map::Gene
Args : -universal_name => string : name of the gene (in a form common to all
species that have the gene, but unique
amongst non-orthologous genes), REQUIRED
-description => string : free text description of the gene
get
Title : get
Usage : my $gene = Bio::Map::Gene->get();
Function: Builds a new Bio::Map::Gene object (like new()), or gets a
pre-existing one that shares the same universal_name.
Returns : Bio::Map::Gene
Args : -universal_name => string, name of the gene (in a form common to all
species that have the gene, but unique amongst
non-orthologous genes), REQUIRED
-description => string, free text description of the gene
universal_name
Title : universal_name
Usage : my $name = $gene->universal_name
Function: Get/Set Mappable name, corresponding to the name of the gene in a
form shared by orthologous versions of the gene in different species,
but otherwise unique.
Returns : string
Args : none to get, OR string to set
description
Title : description
Usage : my $description = $gene->description();
$gene->description($description);
Function: Get/set information relating to the gene, in this case the
description (eg. 'full name of gene')
Returns : string (empty string if not defined)
Args : none to get general version, OR Bio::Map::GeneMap to get map-specific
version.
string to set general version, optionally AND Bio::Map::GeneMap to
set map-specific version
display_id
Title : display_id
Usage : my $display_id = $gene->display_id();
$gene->display_id($display_id);
Function: Get/set information relating to the gene, in this case the
display_id (eg. 'ENSG00000155287')
Returns : string (empty string if not defined)
Args : none to get general version, OR Bio::Map::GeneMap to get map-specific
version.
string to set general version, optionally AND Bio::Map::GeneMap to
set map-specific version
display_xref
Title : display_xref
Usage : my $display_xref = $gene->display_xref();
$gene->display_xref($display_xref);
Function: Get/set information relating to the gene, in this case the
display_xref (eg. 'HUGO:23472').
Returns : string (empty string if not defined)
Args : none to get general version, OR Bio::Map::GeneMap to get map-specific
version.
string to set general version, optionally AND Bio::Map::GeneMap to
set map-specific version
external_db
Title : external_db
Usage : my $external_db = $gene->external_db();
$gene->external_db($external_db);
Function: Get/set information relating to the gene, in this case the
external_db (eg. 'HUGO').
Returns : string (empty string if not defined)
Args : none to get general version, OR Bio::Map::GeneMap to get map-specific
version.
string to set general version, optionally AND Bio::Map::GeneMap to
set map-specific version
external_name
Title : external_name
Usage : my $external_name = $gene->external_name();
$gene->external_name($external_name);
Function: Get/set information relating to the gene, in this case the (eg.
'gene_name', probably the same as or similar to what you set
universal_name() to, but could be a species-specific alternative).
Returns : string (empty string if not defined)
Args : none to get general version, OR Bio::Map::GeneMap to get map-specific
version.
string to set general version, optionally AND Bio::Map::GeneMap to
set map-specific version
biotype
Title : biotype
Usage : my $biotype = $gene->biotype();
$gene->biotype($biotype);
Function: Get/set information relating to the gene, in this case the biotype
(eg. 'protein_coding').
Returns : string (empty string if not defined)
Args : none to get general version, OR Bio::Map::GeneMap to get map-specific
version.
string to set general version, optionally AND Bio::Map::GeneMap to
set map-specific version
source
Title : source
Usage : my $source = $gene->source();
$gene->source($source);
Function: Get/set information relating to the gene, in this case the source
(eg. '??').
Returns : string (empty string if not defined)
Args : none to get general version, OR Bio::Map::GeneMap to get map-specific
version.
string to set general version, optionally AND Bio::Map::GeneMap to
set map-specific version
position
Title : position
Usage : my $position = $mappable->position($map);
Function: Get the main Position of this Mappable on a given map. (A gene may
have many positions on a map, but all but one of them are
Bio::Map::GenePosition objects that describe sub-regions of the gene
which are relative to the 'main' Bio::Map::Position position, which
is the only one that is directly relative to the map - this is the
Position returned by this method.)
Returns : Bio::Map::Position
Args : L<Bio::Map::MapI> object.
add_transcript_position
Title : add_transcript_position
Usage : $gene->add_transcript_position($position);
Function: Set the bounds of a transcript on a map (that of the supplied
position). All transcript positions added this way must have
coordinates relative to the main position of the 'gene' mappable on
this transcript's map. The first position added using this method
must have a start of 0. The supplied Position will be given a type of
'transcript' and relative of (gene => 0). The active_transcript for
the Position's map will be set to this one.
Returns : n/a
Args : Bio::Map::GenePosition (which must have its map() defined, and be for
a map this gene is on)
active_transcript
Title : active_transcript
Usage : my $active = $gene->active_transcript($map);
$gene->active_transcript($map, $int);
Function: Get/set the active transcript number (an int of 1 would mean the 1st
transcript position added to the object for the given map, ie. would
correspond to the the 1st Position object in the list returned by
get_transcript_positions($map)). The active transcript is the one
considered by other methods and objects when dealing with positions
relative to 'the' transcript.
Returns : int, 0 means there were no transcript positions on the given map,
undef is some other problem
Args : Just Bio::Map::GeneMap to get
Bio::Map::GeneMap AND int to set
get_transcript_positions
Title : get_transcript_positions
Usage : my @transcript_positions = $gene->get_transcript_positions($map);
Function: Get all the transcript positions of this gene on the given map, in
the order they were added to the map.
Returns : list of Bio::Map::GenePosition
Args : Bio::Map::GeneMap
get_transcript_position
Title : get_transcript_position
Usage : my $position = $gene->get_transcript_position($map, $int);
Function: Get the $int'th transcript position added to the map. If no
transcripts have been added to the map, and the default transcript
was requested, $gene->position is returned, as that will have the
same start and end as the first transcript.
Returns : Bio::Map::GenePosition
Args : Bio::Map::GeneMap AND int (if int not supplied, or 0, returns
the currently active transcript position)
coding_position
Title : coding_position
Usage : $gene->coding_position($position, $transcript_number);
$gene->coding_position($map, $transcript_number);
Function: Get/set the bounds of a coding region of a given transcript on a map
(that of the supplied position).
When setting, coordinates must be relative to the transcript start.
The supplied position will be given a type 'coding' and a relative
(-transcript => $transcript_number). There can be only one coding
position per transcript (hence this is a get/set).
When getting, if a coding region has not been defined for the
requested transcript, $gene->get_transcript_position($map,
$transcript_number) is returned, as if assuming the entirety of the
transcript is coding.
Returns : Bio::Map::GenePosition
Args : Bio::Map::GeneMap AND int (the transcript number) to get, OR to set:
Bio::Map::GenePosition (which must have its map() defined, and be for
a map this gene is on) AND int (the transcript number)
In both cases, if transcript number not supplied or 0 this will be
resolved to the current active transcript number - there must be at
least one transcript on the map
add_exon_position
Title : add_exon_position
Usage : $gene->add_exon_position($position, $transcript_number);
Function: Set the bounds of an exon of a given transcript on a map (that of the
supplied position). Coordinates must be relative to the transcript
start. The supplied position will be given a type 'exon' and a
relative (-transcript => $transcript_number).
Returns : n/a
Args : Bio::Map::GenePosition (which must have its map() defined, and be for
a map this gene is on) AND int (the transcript number; if not
supplied or 0 this will be resolved to the current active transcript
number - there must be at least one transcript on the map)
get_exon_positions
Title : get_exon_positions
Usage : my @positions = $gene->get_exon_positions($map, $int);
Function: Get all the exon positions that are relative to the $int'th
transcript position added to the map. Exons are returned sorted by
their start positions.
Returns : array of Bio::Map::GenePosition
Args : Bio::Map::GeneMap AND int (the transcript number; if second int not
supplied, or 0, considers the currently active transcript)
get_exon_position
Title : get_exon_position
Usage : my $position = $gene->get_exon_position($map, $exon_num, $int);
Function: Get the $exon_num'th exon position that is relative to the $int'th
transcript position added to the map. Exons are numbered in Position
order, not the order they were added to the map. If no exons have
been added to the map, and the first exon was requested,
$gene->get_transcript_position($map, $int) is returned, as that will
have the same start as the first exon, and could have the same end
for a single exon gene.
Returns : Bio::Map::GenePosition
Args : Bio::Map::GeneMap AND int (the exon you want) AND int (the transcript
number; if second int not supplied, or 0, considers the currently
active transcript)
add_intron_position
Title : add_intron_position
Usage : $gene->add_intron_position($position, $transcript_number);
Function: Set the bounds of an intron of a given transcript on a map (that of
the supplied position). Coordinates must be relative to the
transcript start. The supplied position will be given a type 'intron'
and a relative (-transcript => $transcript_number).
Returns : n/a
Args : Bio::Map::GenePosition (which must have its map() defined, and be for
a map this gene is on) AND int (the transcript number; if not
supplied or 0 this will be resolved to the current active transcript
number - there must be at least one transcript on the map)
get_intron_positions
Title : get_intron_positions
Usage : my @positions = $gene->get_intron_positions($map, $int);
Function: Get all the intron positions that are relative to the $int'th
transcript position added to the map. Introns are returned sorted by
their start positions.
Returns : array of Bio::Map::GenePosition
Args : Bio::Map::GeneMap AND int (the transcript number; if second int not
supplied, or 0, considers the currently active transcript)
get_intron_position
Title : get_intron_position
Usage : my $position = $gene->get_intron_position($map, $intron_num, $int);
Function: Get the $intron_num'th intron position that is relative to the
$int'th transcript position added to the map. Introns are numbered in
Position order, not the order they were added to the map.
Returns : Bio::Map::GenePosition
Args : Bio::Map::GeneMap AND int (the intron you want) AND int (the
transcript number; if second int not supplied, or 0, considers the
currently active transcript)
set_from_db
Title : set_from_db
Usage : $gene->set_from_db(); # for an instance only
Bio::Map::Gene->set_from_db(); # decide that all future genes added
# to maps will be set from db
Function: Creates all the various types of positions (transcripts, coding,
exons, introns) for this gene on all its maps. The information comes
from an Ensembl database via Bio::Tools::Run::Ensembl. NB: will
purge any existing Bio::Map::GenePosition objects that were
previously on the maps this gene is one.
Returns : undef on failure, otherwise the number of maps that successfully
had positions added to them
Args : boolean (no argument/undef is treated as 1, ie. do set from db;
supply 0 to turn off)
NB: Bio::Tools::Run::Ensembl is available in the bioperl-run package;
see it for details on setting up a database to use.
Once set, any new maps (species) this gene is added to will
automatically also have their positions set_from_db