Bio::Map::Gene(3)

NAME
Bio::Map::Gene - An gene modelled as a mappable element.

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.

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 $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