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Bio::NEXUS::SetsBlock 0.67

  Date Added: April 10, 2010  |  Visits: 495

Bio::NEXUS::SetsBlock

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Bio::NEXUS::SetsBlock is a Perl module that represents SETS block of a NEXUS file. SYNOPSIS $block_object = new Bio::NEXUS::SetsBlock($block_type, $block, $verbose); Parses Sets block of NEXUS file and stores Sets data. METHODS new 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) set_taxsets Title : set_taxsets Usage : $block->set_taxsets($taxsets); Function: Set the taxsets hash Returns : none Args : hash of set name keys and element arrays add_taxsets Title : add_taxsets Usage : $block->add_taxsets($taxsets); Function: add taxa sets Returns : none Args : a reference to a hash of taxa sets get_taxsets Title : get_taxsets Usage : $block->get_taxsets(); Function: Returns a hash of taxa sets Returns : taxa sets Args : none get_taxset Title : get_taxset Usage : $block->get_taxset($setname); Function: Returns a list of OTUs Returns : OTUs Args : none get_taxset_names Title : get_taxset_names Usage : $block->get_taxset_names() Function: gets the names of all sets Returns : array of names Args : none print_all_taxsets Title : print_all_taxsets Usage : $block->print_all_taxsets($outfile) Function: prints set names and elements Returns : none Args : filename or filehandle delete_taxsets 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 exclude_otus 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 select_otus 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 rename_otus Title : rename_otus Usage : $block->rename_otus($names); Function: rename all OTUs Returns : none Args : hash of OTU names rename_taxsets Title : rename_taxsets Usage : $block->rename_taxsets($oldsetname1, $newsetname1, ...) Function: Renames sets Returns : none Args : Oldname, newname pairs equals Name : equals Usage : $setsblock->equals($another); Function: compare if two Bio::NEXUS::SetsBlock objects are equal Returns : boolean Args : a Bio::NEXUS::SetsBlock object.

Requirements: No special requirements
Platforms: Linux
Keyword: Args Bionexussetsblock Block Libraries Names Nexus Otus Perl Module Programming Returns Setsblock Title Usage
Users rating: 0/10

License: Freeware Size: 153.6 KB
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