Bio::Map::MapI - Interface for describing Map objects in bioperl
# get a MapI somehowe my $name = $map->name(); # string my $length = $map->length(); # integer my $species= $map->species; # Bio::Species my $type = $map->type(); # genetic/sts/rh/
This object describes the basic functionality of a Map in bioperl. Maps are anything from Genetic Map to Sequence Map to and Assembly Map to Restriction Enzyme to FPC.
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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 jason@bioperl.org
Lincoln Stein, lstein@cshl.org Heikki Lehvaslaiho, heikki@ebi.ac.uk
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : species Usage : my $species = $map->species; Function: Get/Set Species for a map Returns : L<Bio::Species> object Args : (optional) Bio::Species
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 : type Usage : my $type = $map->type Function: Get/Set Map type Returns : String coding map type Args : (optional) string
Title : name Usage : my $name = $map->name Function: Get/Set Map name Returns : Map name Args : (optional) string
Title : length Usage : my $length = $map->length(); Function: Retrieves the length of the map, It is possible for the length to be unknown for maps such as Restriction Enzyme, will return undef in that case Returns : integer representing length of map in current units will return undef if length is not calculateable Args : none
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 : add_element Usage : $map->add_element($marker) Function: Add a Bio::Map::MappableI object to the Map Returns : none Args : Bio::Map::MappableI object
Title : each_element Usage : my @elements = $map->each_element; Function: Retrieves all the elements in a map unordered Returns : Array of Map elements (L<Bio::Map::MarkerI>) Args :
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.