Arlin Stoltzfus > Bio-NEXUS > Bio::NEXUS

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Module Version: 0.78   Source  

NAME ^

Bio::NEXUS - An object-oriented Perl Applications Programming Interface (API) for the NEXUS file format

SYNOPSIS ^

 my $nexus =Bio::NEXUS->new($file); 
 # if $file is not provided, an empty Bio::NEXUS object will be created
 $nexus->write($newfile);

DESCRIPTION ^

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.

FEEDBACK ^

All feedback (bugs, feature enhancements, etc.) are all greatly appreciated.

AUTHORS ^

 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)

METHODS ^

new

 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

get_bionexus_version

 Title   : get_bionexus_version
 Usage   : Bio::NEXUS->get_bionexus_version();
 Function: gets the package version  
 Returns : value of \$VERSION
 Args    : none

read_file

 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

read

 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

create_block

 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

clone

 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

set_name

 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)

get_name

 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

add_comment

 Name    : add_comment
 Usage   : $nexus->add_comment($comment);
 Function: add a block of comments.
 Returns : none
 Args    : a string object

get_comments

 Name    : get_comments
 Usage   : $nexus->get_comments();
 Function: Retrieves all comments.
 Returns : ref to an array of strings
 Args    : none

get_filename

 Name    : get_filename
 Usage   : $nexus->get_filename;
 Function: get the NEXUS filename for this object.
 Returns : A filename
 Args    : none

set_blocks

 Name    : set_blocks
 Usage   : $nexus->set_blocks($blocks);
 Function: set the blocks in this nexus file.
 Returns : none
 Args    : an array of Block objects

add_block

 Name    : add_block
 Usage   : $nexus->add_block($block_obj);
 Function: add a block.
 Returns : none
 Args    : a Bio::NEXUS::*Block object

remove_block

 Name    : remove_block
 Usage   : $nexus->remove_block($blocktype, $title);
 Function: remove a block
 Returns : none
 Args    : block type and block name (strings)

get_block

 Name    : get_block
 Usage   : $nexus->get_block($blocktype, $blockname);
 Function: Retrieves NEXUS block.
 Returns : A Bio::NEXUS::*Block object
 Args    : none

get_blocks

 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

get_blocks_and_comments

 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

get_weights

 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

get_taxlabels

 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

get_otus

 Name    : get_otus
 Usage   : $nexus->get_otus();
 Function: Retrieves list of OTUs 
 Returns : Array of OTU names or Bio::NEXUS::TaxUnit objects
 Args    : none

rename_otus

 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

add_otu_clone

 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)

select_blocks

 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

exclude_blocks

 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

select_otus

 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

exclude_otus

 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

select_tree

 Name    : select_tree
 Usage   : $nexus->select_tree($treename);
 Function: select a tree
 Returns : a new nexus object 
 Args    : a tree name

select_subtree

 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

exclude_subtree

 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

select_chars

 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

exclude_chars

 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

reroot

 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

equals

 Name    : equals
 Usage   : $nexus->equals($another);
 Function: compare if two Bio::NEXUS objects are equal
 Returns : boolean 
 Args    : a Bio::NEXUS object

write

 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

set_taxablock

 Name    : set_taxablock
 Usage   : $nexus->set_taxablock();
 Function: Sets taxablock if taxablock is not already defined in the nexus object
 Returns : none
 Args    : none
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