Bio::Map::CytoMap - A Bio::MapI compliant map implementation handling cytogenic bands
use Bio::Map::CytoMap; my $map = new Bio::Map::CytoMap(-name => 'human1', -species => $human); foreach my $marker ( @markers ) { # get a list of markers somewhere $map->add_element($marker); }
This is the simple implementation of cytogenetic maps based on Bio::Map::MapI. It handles the essential storage of name, species, type, and units as well as in memory representation of the elements of a map.
For CytoMaps type is hard coded to be 'cytogeneticmap' and units are set to '' but can be set to something else.
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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 email or the web:
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Email heikki@ebi.ac.uk
Jason Stajich jason@bioperl.org Lincoln Stein lstein@cshl.org
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
All methods present in Bio::Map::SimpleMap are implemted by this class. Most of the methods are inherited from SimpleMap. The following methods have been modified to refelect the needs of cytogenetic maps.
Title : new Usage : my $obj = new Bio::Map::CytoMap(); Function: Builds a new Bio::Map::CytoMap object Returns : Bio::Map::CytoMap Args : -name => name of map (string) -species => species for this map (Bio::Species) [optional] -elements=> elements to initialize with (arrayref of Bio::Map::MappableI objects) [optional] -uid => Unique Id
Title : type Usage : my $type = $map->type Function: Get hard-coded Map type Returns : String coding map type Args :
Title : length Usage : my $length = $map->length(); Function: Retrieves the length of the map, Returns : undef since length is not calculatable for cytogenetic maps Args : none
Title : species Usage : my $species = $map->species; Function: Get/Set Species for a map Returns : Bio::Species object or string Args : (optional) Bio::Species or string
Title : units Usage : $map->units('cM'); Function: Get/Set units for a map Returns : units for a map Args : units for a map (string)
Title : name Usage : my $name = $map->name Function: Get/Set Map name Returns : Map name Args : (optional) string
Title : unique_id Usage : my $id = $map->unique_id; Function: Get/Set the unique ID for this map Returns : a unique identifier Args : [optional] new identifier to set
Title : each_element Usage : my @elements = $map->each_element; Function: Retrieves all the elements in a map unordered Returns : Array of Bio::Map::MappableI objects Args : none
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.