Free bio phylo io 0.17 rc6 software for linux

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

Bio::Phylo::Treedrawer::Svg is a Perl module that creates svg tree drawings. No serviceable parts inside.

This module creates a scalable vector graphic from a Bio::Phylo::Trees::Tree object. It is called by the Bio::Phylo::Treedrawer object, so look there to learn how to create tree drawings. (For extra per-node formatting, attach a hash reference to the node, like so: $node->set_generic( svg => { stroke => red } ), which outlines the node, and branch leading up to it, in red.)

Bio::PopGen::IO contains input individual,marker,allele information.

SYNOPSIS

use Bio::PopGen::IO;
my $io = new Bio::PopGen::IO(-format => csv,
-file => data.csv);

# Some IO might support reading in a population at a time

my @population;
while( my $ind = $io->next_individual ) {
push @population, $ind;
}

This is a generic interface to reading in population genetic data (of which there really isnt too many standard formats). This implementation makes it easy to provide your own parser for the data. You need to only implement one function next_individual. You can also implement next_population if your data has explicit information about population memberhsip for the indidviduals.

Bio::NEXUS::HistoryBlock is a Perl module that represents a HISTORY block of a NEXUS file.

SYNOPSIS

$block_object = new Bio::NEXUS::HistoryBlock(history, $block, $verbose);

This is a class representing a history block in NEXUS file

METHODS

new

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

equals

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

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

Bio::Graphics::Panel is a Perl module to generate GD images of Bio::Seq objects.

SYNOPSIS

# This script parses a GenBank or EMBL file named on the command
# line and produces a PNG rendering of it. Call it like this:
# render.pl my_file.embl | display -

use strict;
use Bio::Graphics;
use Bio::SeqIO;

my $file = shift or die "provide a sequence file as the argument";
my $io = Bio::SeqIO->new(-file=>$file) or die "could not create Bio::SeqIO";
my $seq = $io->next_seq or die "could not find a sequence in the file";

my @features = $seq->all_SeqFeatures;

# sort features by their primary tags
my %sorted_features;
for my $f (@features) {
my $tag = $f->primary_tag;
push @{$sorted_features{$tag}},$f;
}

my $panel = Bio::Graphics::Panel->new(
-length => $seq->length,
-key_style => between,
-width => 800,
-pad_left => 10,
-pad_right => 10,
);
$panel->add_track( arrow => Bio::SeqFeature::Generic->new(-start=>1,
-end=>$seq->length),
-bump => 0,
-double=>1,
-tick => 2);
$panel->add_track(generic => Bio::SeqFeature::Generic->new(-start=>1,
-end=>$seq->length),
-glyph => generic,
-bgcolor => blue,
-label => 1,
);

# general case
my @colors = qw(cyan orange blue purple green chartreuse magenta yellow aqua);
my $idx = 0;
for my $tag (sort keys %sorted_features) {
my $features = $sorted_features{$tag};
$panel->add_track($features,
-glyph => generic,
-bgcolor => $colors[$idx++ % @colors],
-fgcolor => black,
-font2color => red,
-key => "${tag}s",
-bump => +1,
-height => 8,
-label => 1,
-description => 1,
);
}

print $panel->png;
$panel->finished;

exit 0;

The Bio::Graphics::Panel class provides drawing and formatting services for any object that implements the Bio::SeqFeatureI interface, including Ace::Sequence::Feature and Das::Segment::Feature objects. It can be used to draw sequence annotations, physical (contig) maps, or any other type of map in which a set of discrete ranges need to be laid out on the number line.

The module supports a drawing style in which each type of feature occupies a discrete "track" that spans the width of the display. Each track will have its own distinctive "glyph", a configurable graphical representation of the feature.
The module also supports a more flexible style in which several different feature types and their associated glyphs can occupy the same track. The choice of glyph is under run-time control.

Semantic zooming (for instance, changing the type of glyph depending on the density of features) is supported by a callback system for configuration variables. The module has built-in support for Bio::Das stylesheets, and stylesheet-driven configuration can be intermixed with semantic zooming, if desired.

You can add a key to the generated image using either of two key styles. One style places the key captions at the top of each track. The other style generates a graphical key at the bottom of the image.

Note that this module depends on GD. The optional SVG output depends on GD::SVG and SVG.

Bio::NEXUS::Functions is a Perl module that provides private utility functions for the module.

This package provides private functions that are not object-specific.

Bio::NEXUS::DataBlock is a Perl module that represents the deprecated DATA Block in NEXUS file.

SYNOPSIS

$block_object = new Bio::NEXUS::DataBlock($type, $block, $verbose, $taxlabels_ref);

The DataBlock class represents the deprecated Data Block in a NEXUS file. Data Blocks are still used by some prominent programs, unfortunately, although they are essentially the same as a Characters Block and a Taxa Block combined. Data Blocks may be used as input, but are not output by the NEXPL library. For more information on Data Blocks, see the Characters Block documentation.

METHODS

new

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

Bio::NEXUS::NotesBlock is a Perl module that represents a NOTES block in a NEXUS file.

Placeholding module for the Notes Block class.