Provided by: libbio-perl-perl_1.6.923-1_all bug

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:

         https://redmine.open-bio.org/projects/bioperl/

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 arguments.
        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)