Bio::Map::GeneMap.3pm

Langue: en

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

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Map::GeneMap - A MapI implementation to represent the area around a gene

SYNOPSIS

     use Bio::Map::GeneMap;
     use Bio::Map::Gene;
     use Bio::Map::TranscriptionFactor;
     use Bio::Map::GeneRelative;
 
         # make some maps that will represent an area around a particular gene in
         # particular species (by default, the map represents the area in the genome
     # 1000bp upstream of the gene)
     my $map1 = Bio::Map::GeneMap->get(-gene => 'BRCA2',
                                       -species => 'human',
                                       -description => 'breast cancer 2, early onset');
         my $map2 = Bio::Map::GeneMap->get(-gene => 'BRCA2',
                                       -species => 'mouse');
 
         # model a TF that binds 500bp upstream of the BRCA2 gene in humans and
         # 250bp upstream of BRCA2 in mice
         my $rel = Bio::Map::GeneRelative->new(-description => "gene start");
     my $tf = Bio::Map::TranscriptionFactor->get(-universal_name => 'tf1');
         Bio::Map::Position->new(-map => $map1,
                             -element => $tf,
                             -start => -500,
                             -length => 10,
                             -relative => $rel);
         Bio::Map::Position->new(-map => $map2,
                             -element => $tf,
                             -start => -250,
                             -length => 10,
                             -relative => $rel);
 
         # find out all the things that map near BRCA2 in all species
         foreach my $map ($gene->known_maps) {
                 foreach my $thing ($map->get_elements) {
             next if $thing eq $gene;
             foreach my $pos ($thing->get_positions($map)) {
                 print "In species ", $map->species, ", ",
                       $thing->universal_name, " maps at ", $pos->value,
                       " relative to ", $pos->relative->description, " of gene ",
                       $gene->universal_name, "\n";
             }
                 }
         }
     
     # a GeneMap isa PrimarySeq and so can have sequence associated with it
     $map1->seq('ATGC');
     my $subseq = $map1->subseq(2,3); # TG
 
 

DESCRIPTION

Model the abstract notion of the area around a gene - you don't care exactly where this area is in the genome, you just want to be able to say ``something binds upstream of gene X'' and ``something else binds 20bp upstream of the first something'' etc.

It's useful for modelling transcription factor bindings sites, letting you find out which transcription factors bind near a gene of interest, or which genes are bound by a transcription factor of interest.

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 $obj = Bio::Map::GeneMap->new();
  Function: Builds a new Bio::Map::GeneMap object (that has placed on it a
            mappable element (Bio::Map::Gene) representing a gene).
  Returns : Bio::Map::GeneMap
  Args    : -gene        => string name of the gene this map will be for
                            (in a form common to all species that have the gene,
                            but unique amongst non-orthologous genes) or a
                            Bio::Map::Gene object, REQUIRED
            -species     => Bio::Taxon or string representing species, REQUIRED
            -uid         => string, unique identifier for this map (must be
                            unique amongst all gene/species combinations)
            -description => string, free text description of the gene
            -upstream    => int, the number of bases the map extends before the
                            start of the gene element (default 1000).
            -downstream  => int, the number of bases the map extends beyond the
                            end of the gene element (default 0).
            -seq         => string, the sequence of the map, presumably the
                            genomic sequence -upstream bases of the gene,
                            including the gene, and -downstream bases of the gene
 
 

get

  Title   : get
  Usage   : my $map = Bio::Map::GeneMap->get();
  Function: Builds a new Bio::Map::GeneMap object (like new()), or gets a
            pre-existing one that corresponds to your arguements.
  Returns : Bio::Map::GeneMap
  Args    : -gene        => string name of the gene this map will be for
                            (in a form common to all species that have the gene,
                            but unique amongst non-orthologous genes) or a
                            Bio::Map::Gene object, REQUIRED
            -species     => Bio::Taxon or string representing species, REQUIRED
            -uid         => string, unique identifier for this map (must be
                            unique amongst all gene/species combinations)
            -description => string, free text description of the gene
            -upstream    => int, the number of bases the map extends before the
                            start of the gene element (default 1000).
            -downstream  => int, the number of bases the map extends beyond the
                            end of the gene element (default 0).
            -seq         => string, the sequence of the map, presumably the
                            genomic sequence -upstream bases of the gene,
                            including the gene, and -downstream bases of the gene
 
            If you supply a -uid, and a map had previously been created and
            given that uid, that same map object will be returned. Otherwise, the
            combination of -gene and -species will be used to determine
            if the same map had previously been made. If a corresponding map
            hadn't previously been made, a new map object will be created and
            returned.
 
 

unique_id

  Title   : unique_id
  Usage   : my $id = $map->unique_id;
  Function: Get/set the unique ID for this map
  Returns : string
  Args    : none to get, OR string to set
 
 

species

  Title   : species
  Usage   : my $species = $map->species;
  Function: Get/set Species for a map. It is not recommended to change this once
            set.
  Returns : Bio::Taxon object or string
  Args    : none to get, OR Bio::Taxon or string to set
 
 

type

  Title   : type
  Usage   : my $type = $map->type
  Function: Get Map type
  Returns : string 'gene'
  Args    : none
 
 

gene

  Title   : gene
  Usage   : my $gene = $map->gene;
            $map->gene(-gene => $gene);
  Function: Get/set the mappable element on this map that represents the gene
            this map is for. Once set, it is not recommended to re-set the gene
            to something else. Behaviour in that case is undefined.
  Returns : Bio::Map::Gene
  Args    : none to get, OR to set:
            -gene        => Bio::Map::Gene or string of the universal name (see
                            Bio::Map::Gene docs), REQUIRED
            -description => string, applied to the Bio::Map::Gene
            -upstream    => int, the number of bases the map extends before the
                            start of the gene element (default 1000).
            -downstream  => int, the number of bases the map extends beyond the
                            end of the gene element (default 0).
 
 

universal_name

  Title   : universal_name
  Usage   : my $name = $map->universal_name
  Function: Get/set the name of Bio::Map::Gene object associated with this map.
            It is not recommended to change this once set.
  Returns : string
  Args    : none to get, OR string to set
 
 

upstream

  Title   : upstream
  Usage   : my $distance = $map->upstream;
            $map->upstream($distance);
  Function: Get/set how long the map is before the start of the Bio::Map::Gene
            object on this map.
  Returns : int
  Args    : none to get, OR int to set (the number of bases the map extends
            before the start of the gene)
 
 

downstream

  Title   : downstream
  Usage   : my $distance = $map->downstream;
            $map->downstream($distance);
  Function: Get/set the nominal end of the map relative to the end of the
            Bio::Map::Gene object on this map.
  Returns : int
  Args    : none to get, OR int to set (the number of bases the map extends
            beyond the end of the gene)
 
 

length

  Title   : length
  Usage   : my $length = $map->length();
  Function: Retrieves the length of the map. This is normally the length of the
            upstream region + length of the gene + length of the downstream
            region, but may be longer if positions have been placed on the map
            beyond the end of the nominal downstream region.
  Returns : int
  Args    : none
 
 

seq

  Title   : seq
  Usage   : $string = $obj->seq()
  Function: Get/set the sequence as a string of letters. When getting, If the
            GeneMap object didn't have sequence attached directly to it for the
            region requested, the map's gene's database will be asked for the
            sequence, and failing that, the map's gene's positions will be asked
            for their sequences. Areas for which no sequence could be found will
            be filled with Ns, unless no sequence was found anywhere, in which
            case undef is returned.
  Returns : string
  Args    : Optionally on set the new value (a string). An optional second
            argument presets the alphabet (otherwise it will be guessed).
 
 

subseq

  Title   : subseq
  Usage   : $substring = $obj->subseq(10, 40);
  Function: Returns the subseq from start to end, where the first base
            is 1 and the number is inclusive, ie 1-2 are the first two
            bases of the sequence. If the GeneMap object didn't have sequence
            attached directly to it for the region requested, the map's gene's
            database will be asked for the sequence, and failing that, the map's
            gene's positions will be asked for their sequences. Areas for which
            no sequence could be found will be filled with Ns, unless no
            sequence was found anywhere, in which case undef is returned. subseq
            requests that extend beyond the end of the map will throw.
  Returns : string
  Args    : integer for start position AND integer for end position
                  OR
            Bio::LocationI location for subseq (strand honored)
                  OR
            Bio::RangeI (eg. a Bio::Map::PositionI)