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.
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
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/
Email heikki-at-bioperl-dot-org
Jason Stajich jason@bioperl.org Lincoln Stein lstein@cshl.org Sendu Bala bix@sendu.me.uk
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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 (always 'cyto') Args : none
Title : length Usage : my $length = $map->length(); Function: Retrieves the length of the map, Returns : 0 since length is not calculatable for cytogenetic maps 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.