Free taxa software for linux

Bio::NEXUS::TaxaBlock is a Perl module that represents TAXA block of a NEXUS file.

SYNOPSIS

if ( $type =~ /taxa/i ) {
$block_object = new Bio::NEXUS::TaxaBlock($type, $block, $verbose);
}

If a NEXUS block is a taxa block, this module parses the block and stores the taxonomic data.

METHODS

new

Title : new
Usage : block_object = new Bio::NEXUS::TaxaBlock($block_type, $commands, $verbose);
Function: Creates a new Bio::NEXUS::TaxaBlock object
Returns : Bio::NEXUS::TaxaBlock object
Args : type (string), the commands/comments to parse (array ref), and a verbose flag (0 or 1; optional)

is_taxon

Title : is_taxon
Usage : $block->is_taxon($query_taxonlabel);
Function: Validates OTU names/taxlabels
Returns : Returns taxlabel if true, undef if false
Args : Query taxon label

get_ntax

Title : get_ntax
Usage : $block->get_ntax();
Function: Returns the dimensions (that is, ntax) of the block
Returns : dimensions (integer)
Args : none

rename_otus

Title : rename_otus
Usage : $block->rename_otus(%translation);
Function: Renames all the OTUs to something else
Returns : none
Args : hash containing translation

equals

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

Bio::NEXUS::MatrixBlock is a Perl module that provides functions for handling blocks that have matrices.

SYNOPSIS

This module is the super class of Characters, Unaligned, and Distances block classes, and indirectly it is a super-class of Data and History blocks, which are both sub-classes of Characters blocks. These sub-classes inherint the methods within this module. There is no constructor, as a MatrixBlock should not exist that is not also one of the sub-class block types.

Provides functions used for handling blocks that have matrices.

METHODS

get_ntax

Title : get_ntax
Usage : $block->get_ntax();
Function: Returns the number of taxa in the block
Returns : # taxa
Args : none

get_nchar

Title : get_nchar
Usage : $block->get_nchar();
Function: Returns the number of characters in the block (Note: In Distances Blocks, this is the number of characters used to infer distances.)
Returns : # taxa
Args : none

set_format

Title : set_format
Usage : $block->set_format(%format);
Function: set the format of the characters
Returns : none
Args : hash of format values

get_format

Title : get_format
Usage : $block->get_format($attribute);
Function: Returns the format of the characters
Returns : hash of format values, or if $attribute (a string) is supplied, the value of that attribute in the hash
Args : none

add_taxlabels

Title : add_taxlabels
Usage : $block->add_taxlabels($new_taxlabels);
Function: Adds new taxa to taxlabels if they arent already there
Returns : none
Args : taxa to be added

Bio::NEXUS::DistancesBlock is a Perl module that represents DISTANCES block in NEXUS file.

The DistancesBlock class represents a NEXUS Distances Block and provides methods for reading, writing, and accessing data within these blocks. Distances Blocks contain distance matrices, or a table of calculated distances between each possible pair of taxa.

METHODS

new

Title : new
Usage : block_object = new Bio::NEXUS::DistancesBlock($block_type, $commands, $verbose, $taxa);
Function: Creates a new Bio::NEXUS::DistancesBlock object
Returns : Bio::NEXUS::DistancesBlock object
Args : type (string), the commands/comments to parse (array ref), and a verbose flag (0 or 1)

get_matrix

Title : get_matrix
Usage : $matrix = $self->get_matrix();
Function: Retrieves the entire distance matrix
Returns : a hashref of hashrefs
Args : none
Note : Distance values may be retrieved by specifying the row and column keys, e.g. $dist = $matrix->{$row_taxon}{$col_taxon}

get_distances_for

Title : get_distances_for
Usage : %taxon1_distances = %{ $self->get_distances_for($first_taxon) };
Function: Retrieves a row of the distance matrix
Returns :
Args : the row label (a taxlabel) for the row desired (string)

get_distance_between

Title : get_distance_between
Usage : $distance = $self->get_distance_between($row_taxon, $column_taxon);
Function: Retrieves a cell from the matrix
Returns : A scalar (number)
Args : the row and column labels (both taxa) for the cell desired
Note : Generally get_distance_between($A, $B) == get_distance_between($B, $A); however, this need not be true if the distance matrix is not symmetric. Make sure you are asking for the distance you want.

Bio::NEXUS::Block is a Perl module that provides useful functions for blocks in NEXUS file (parent class).

SYNOPSIS

This module is the super class of all NEXUS block classes. It is not used specifically from a program; in other words, you dont create a new Bio::NEXUS::Block object. Other modules, like AssumptionsBlock, simply inherit subroutines from this module.

Provides a few useful functions for general blocks (to be used by sub-classes).

METHODS

clone

Title : clone
Usage : my $newblock = $block->clone();
Function: clone a block object (shallow)
Returns : Block object
Args : none

get_type

Title : get_type
Usage : print $block->get_type();
Function: Returns a string containing the block type
Returns : type (string)
Args : none

set_ntax

Title : set_ntax
Usage : print $block->set_ntax();
Function: Sets the value of Dimensions:ntax
Returns : none
Args : number of taxa (scalar)

set_dimensions

Title : set_dimensions
Usage : $block->set_dimensions($dimensions);
Function: set a dimensions command
Returns : none
Args : hash content of dimensions command

get_dimensions

Title : get_dimensions
Usage : $block->get_dimensions($attribute);
Function: get a dimensions command
Returns : hash content of dimensions command, or the value for a particular attribute if specified
Args : none, or a string

set_command

Title : set_command
Usage : $block->set_command($command, $content);
Function: Set a command
Returns : none
Args : comand name, and content (string)

set_title

Title : set_title
Usage : $block->set_title($name);
Function: Set the block name
Returns : none
Args : block name (string)

get_title

Title : get_title
Usage : $block->get_title();
Function: Returns a string containing the block title
Returns : name (string)
Args : none

set_link

Title : set_link
Usage : $block->set_link($link_hashref);
Function: Set the block link commands
Returns : none
Args : block link (hash)

add_link

Title : add_link
Usage : $block->add_link($linkname, $title);
Function: add a link command
Returns : none
Args : $link, $title (of another block)

get_link

Title : get_link
Usage : $block->get_link();
Function: Returns a hash containing the block links
Returns : link (hash)
Args : none

set_taxlabels

Title : set_taxlabels
Usage : $block->set_taxlabels($labels);
Function: Set the taxa names
Returns : none
Args : array of taxa names

add_taxlabel

Title : add_taxlabel
Usage : $block->add_taxlabel($label);
Function: add a taxon name
Returns : none
Args : a taxon name

get_taxlabels

Title : get_taxlabels
Usage : $block->get_taxlabels();
Function: Returns an array of taxa labels
Returns : taxa names
Args : none

set_otus

Title : set_otus
Usage : $block->set_otus($otus);
Function: sets the list of OTUs
Returns : none
Args : array of OTUs

get_otus

Title : get_otus
Usage : $block->get_otus();
Function: Returns array of otus
Returns : all otus
Args : none

set_otuset

Title : set_otuset
Usage : $block->set_otuset($otuset);
Function: Set the otus
Returns : none
Args : TaxUnitSet object

get_otuset

Title : get_otuset
Usage : $block->get_otuset();
Function: get the OTUs
Returns : TaxUnitSet object
Args : none

select_otus

Title : select_otus
Usage : $block->select_otus($names);
Function: select a subset of OTUs
Returns : array of OTUs
Args : OTU names

rename_otus

Title : rename_otus
Usage : $block->rename_otus($names);
Function: rename all OTUs
Returns : none
Args : hash of OTU names

set_comments

Title : set_comments
Usage : $block->set_comments($comments);
Function: Set the block comments
Returns : none
Args : block comments (array of strings)

get_comments

Title : get_comments
Usage : $block->get_comments();
Function: Returns block comments
Returns : comments (array of strings)
Args : none

add_comment

Title : add_comment
Usage : $block->add_comment($comment);
Function: add a comment
Returns : none
Args : comment (string)

equals

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

Bio::Phylo::IO Perl module contains input and output of phylogenetic data.

SYNOPSIS

use Bio::Phylo::IO;

# parsing a tree from a newick string
my $tree_string = (((A,B),C),D);;
my $tree = Bio::Phylo::IO->parse(
-string => $tree_string,

# old parser, always adds node labels
-format => newick,
)->first;

# note: newick parsers return
# Bio::Phylo::Forest! Call
# ->first to retrieve the first
# tree of the forest.

# prints Bio::Phylo::Forest::Tree
print ref $tree, "n";

# parsing a table
my $table_string = qq(A,1,2|B,1,2|C,2,2|D,2,1);
my $matrix = Bio::Phylo::IO->parse(
-string => $table_string,
-format => table,

# Data type, see Bio::Phylo::Parsers::Table
-type => STANDARD,

# field separator
-fieldsep => ,,

# line separator
-linesep => |
);

# prints Bio::Phylo::Matrices::Matrix
print ref $matrix, "n";

# parsing a list of taxa
my $taxa_string = A:B:C:D;
my $taxa = Bio::Phylo::IO->parse(
-string => $taxa_string,
-format => taxlist,
-fieldsep => :
);

# prints Bio::Phylo::Taxa
print ref $taxa, "n";

# matches taxon names in tree to $taxa object
$tree->cross_reference($taxa);

# likewise for matrix
$matrix->cross_reference($taxa);

print Bio::Phylo::IO->unparse(

# pass the tree object,
# crossreferenced to taxa, which
# are crossreferenced to the matrix
-phylo => $tree,
-format => pagel
);

# prints a pagel data file:
#4 2
#A,n1,0.000000,1,2
#B,n1,0.000000,1,2
#n1,n2,0.000000
#C,n2,0.000000,2,2
#n2,n3,0.000000
#D,n3,0.000000,2,1