/ 
Bio-NEXUS-0.67
River stage one • 1 direct dependent • 1 total dependent
/ Bio::NEXUS

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

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' => $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

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