Bio::NEXUS::SetsBlock - Represents SETS block of a NEXUS file
$block_object = new Bio::NEXUS::SetsBlock($block_type, $block, $verbose);
Parses Sets block of NEXUS file and stores Sets data.
All feedback (bugs, feature enhancements, etc.) are greatly appreciated.
Thomas Hladish (tjhladish at yahoo)
$Revision: 1.32 $
Title : new Usage : $block_object = new Bio::NEXUS::SetsBlock($block_type, $commands, $verbose) Function: Creates a new Bio::NEXUS::SetsBlock object Returns : Bio::NEXUS::SetsBlock object Args : type (string), the commands/comments to parse (array ref), and a verbose flag (0 or 1)
Title : set_taxsets Usage : $block->set_taxsets($taxsets); Function: Set the taxsets hash Returns : none Args : hash of set name keys and element arrays
Title : add_taxsets Usage : $block->add_taxsets($taxsets); Function: add taxa sets Returns : none Args : a reference to a hash of taxa sets
Title : get_taxsets Usage : $block->get_taxsets(); Function: Returns a hash of taxa sets Returns : taxa sets Args : none
Title : get_taxset Usage : $block->get_taxset($setname); Function: Returns a list of OTU's Returns : OTU's Args : none
Title : get_taxset_names Usage : $block->get_taxset_names() Function: gets the names of all sets Returns : array of names Args : none
Title : print_all_taxsets Usage : $block->print_all_taxsets($outfile) Function: prints set names and elements Returns : none Args : filename or filehandle
Title : delete_taxsets Usage : $block->delete_taxsets($set1 [$set2 $set3 ...]) Function: Removes the named sets from the Sets block Returns : none Args : Names of sets to be deleted
Title : exclude_otus Usage : $block->exclude_otus($otu_array_ref) Function: Finds and deletes each of the given otus from any sets they appear in Returns : none Args : Names of otus to be removed
Title : select_otus Usage : $block->select_otus($otu_array_ref) Function: Finds the given otus and removes all others from any sets they appear in Returns : none Args : Names of otus to be removed
Title : rename_otus Usage : $block->rename_otus($names); Function: rename all OTUs Returns : none Args : hash of OTU names
Title : add_otu_clone Usage : ... Function: ... Returns : ... Args : ...
Title : rename_taxsets Usage : $block->rename_taxsets($oldsetname1, $newsetname1, ...) Function: Renames sets Returns : none Args : Oldname, newname pairs
Name : equals Usage : $setsblock->equals($another); Function: compare if two Bio::NEXUS::SetsBlock objects are equal Returns : boolean Args : a Bio::NEXUS::SetsBlock object
To install Bio::NEXUS, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::NEXUS
CPAN shell
perl -MCPAN -e shell install Bio::NEXUS
For more information on module installation, please visit the detailed CPAN module installation guide.