Bio::NEXUS - An object-oriented Perl Applications Programming Interface (API) for the NEXUS file format
my $nexus =Bio::NEXUS->new($file); # if $file is not provided, an empty Bio::NEXUS object will be created $nexus->write($newfile);
This is the base class for the Bio::NEXUS package, providing an object-oriented API to the NEXUS file format of Maddison, et al., 1997. This module provides methods to add/remove blocks, select blocks/trees/subtrees/OTUs/characters and so on. For a tutorial illustrating how to use Bio::NEXUS, see "Tutorial.pod" in doc.
All feedback (bugs, feature enhancements, etc.) are all greatly appreciated.
Chengzhi Liang (liangc@umbi.umd.edu) Weigang Qiu (weigang@genectr.hunter.cuny.edu) Peter Yang (pyang@rice.edu) Thomas Hladish (tjhladish at yahoo) Arlin Stoltzfus (arlin.stoltzfus@nist.gov)
Title : new Usage : my $nexus = Bio::NEXUS->new($filename, $verbose); Function: Creates a new Bio::NEXUS object Returns : Bio::NEXUS object Args : $filename, $verbose, or none
Title : read_file Usage : Bio::NEXUS->read_file($filename, $verbose); Function: Reads the contents of the NEXUS file and populate the data in the Bio::NEXUS object Returns : None Args : $filename, $verbose, or none
Title : read Usage : Bio::NEXUS->read({format => 'string', 'param' => $buffer, 'verbose' => $verbose}); Usage : Bio::NEXUS->read({format => 'file', 'param' => $filename, 'verbose' => $verbose}); Function: Reads the contents of the NEXUS file and populate the data in the NEXUS object Returns : None Args : $filename, $verbose, or none
Title : create_block Usage : my $block = Bio::NEXUS->create_block($blocktype,$block_string, $verbose); Function: Creates a block object based on the input block type and block content as string Returns : A block object (If Block type is 'Characters' then 'Bio::NEXUS::CharactersBlock' is returned Args : $block_type (as string), $block_content (as string), verbose
Name : clone Usage : my $newnexus = $nexus->clone(); Function: clone a NEXUS object; each block is also (shallow) cloned. Returns : new Bio::NEXUS object Args : none
Title : set_name Usage : Bio::NEXUS->set_name($name); Function: Sets name for the NEXUS object (usually the filename). Returns : Nothing Args : $name (as string)
Title : get_name Usage : $name = Bio::NEXUS->get_name(); Function: Returns the name of the NEXUS object as string. (NEXUS filename). Returns : NEXUS filename Args : None
Name : add_comment Usage : $nexus->add_comment($comment); Function: add a block of comments. Returns : none Args : a string object
Name : get_comments Usage : $nexus->get_comments(); Function: Retrieves all comments. Returns : ref to an array of strings Args : none
Name : get_filename Usage : $nexus->get_filename; Function: get the NEXUS filename for this object. Returns : A filename Args : none
Name : set_blocks Usage : $nexus->set_blocks($blocks); Function: set the blocks in this nexus file. Returns : none Args : an array of Block objects
Name : add_block Usage : $nexus->add_block($block_obj); Function: add a block. Returns : none Args : a Bio::NEXUS::*Block object
Name : remove_block Usage : $nexus->remove_block($blocktype, $title); Function: remove a block Returns : none Args : block type and block name (strings)
Name : get_block Usage : $nexus->get_block($blocktype, $blockname); Function: Retrieves NEXUS block. Returns : A Bio::NEXUS::*Block object Args : none
Name : get_blocks Usage : $nexus->get_blocks($blocktype); Function: Retrieves list of blocks of some type or all blocks. Returns : Array of Bio::NEXUS::Block objects Args : $blocktype or none
Name : get_blocks_and_comments Usage : @blocks_and_comments = @{ $nexus->get_blocks_and_comments() }; Function: get all comments and blocks in the NEXUS object Returns : array of strings and block objects Args : none
Name : get_weights Usage : $nexus->get_weights($charblockname); Function: get all weights for a block. Returns : the weights of alignments in a Characters Block Args : an hash of weightset objects
Name : get_taxlabels Usage : $nexus->get_taxlabels(); Function: get the taxa labels of the NEXUS object (obtained from TAXA block). Returns : an arrayreference of taxa labels. Args : none
Name : get_otus Usage : $nexus->get_otus(); Function: Retrieves list of OTUs Returns : Array of OTU names or Bio::NEXUS::TaxUnit objects Args : none
Name : rename_otus Usage : $nexus->rename_otus(\%translation); Function: rename all OTUs Returns : a new nexus object with new OTU names Args : a ref to hash based on OTU name pairs
Name : add_otu_clone Usage : $nexus_object->add_otu_clone($original_otu_name, $copy_otu_name); Function: creates a copy of a specified otu inside this Bio::NEXUS object Returns : n/a Args : $original_otu_name (string) - the name of the otu that will be cloned, $copy_otu_name (string) - the desired name for the new clone Preconditions : $original_otu_name and $copy_otu_name are not equal, $original_otu_name is a valid otu name (existing otu)
Name : select_blocks Usage : $nexus->select_blocks(\@blocknames); Function: select a subset of blocks Returns : a new nexus object Args : a ref to array of block names to be selected
Name : exclude_blocks Usage : $nexus->exclude_blocks(\@blocknames); Function: remove a subset of blocks Returns : a new nexus object Args : a ref to array of block names to be removed
Name : select_otus Usage : $nexus->select_otus(\@otunames); Function: select a subset of OTUs Returns : a new nexus object Args : a ref to array of OTU names
Name : exclude_otus Usage : $nexus->exclude_otus(\@otunames); Function: remove a subset of OTUs Returns : a new nexus object Args : a ref to array of OTU names to be removed
Name : select_tree Usage : $nexus->select_tree($treename); Function: select a tree Returns : a new nexus object Args : a tree name
Name : select_subtree Usage : $nexus->select_subtree($inodename); Function: select a subtree Returns : a new nexus object Args : an internal node name for subtree to be selected
Name : exclude_subtree Usage : $nexus->exclude_subtree($inodename); Function: remove a subtree Returns : a new nexus object Args : an internal node for subtree to be removed
Name : select_chars Usage : $nexus->select_chars(\@columns); Function: select a subset of characters Returns : a new nexus object Args : a ref to array of character columns
Name : exclude_chars Usage : $nexus->exclude_chars($columns,block_type); Function: exclude specified columns from a block. Returns : new nexus object Args : column numbers to exclude as array reference, block_type as string
Name : reroot Usage : $nexus->reroot($outgroupname); Function: reroot the tree using the new outgroup Returns : a new nexus object Args : a OTU name as new outgroup
Name : equals Usage : $nexus->equals($another); Function: compare if two Bio::NEXUS objects are equal Returns : boolean Args : a Bio::NEXUS object
Name : write Usage : $nexus->write($filename, $verbose); Function: Writes to NEXUS file from stored NEXUS data Returns : none Args : file name (string) for output to file or '-' or 'STDOUT' for standard output
Name : set_taxablock Usage : $nexus->set_taxablock(); Function: Sets taxablock if taxablock is not already defined in the nexus object Returns : none Args : none
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.