Bio::Map::Gene.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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