/
newick.rb
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/
newick.rb
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#
# = bio/db/newick.rb - Newick Standard phylogenetic tree parser / formatter
#
# Copyright:: Copyright (C) 2004-2006
# Naohisa Goto <ng@bioruby.org>
# Daniel Amelang <dan@amelang.net>
# License:: The Ruby License
#
# $Id:$
#
# == Description
#
# This file contains parser and formatter of Newick and NHX.
#
# == References
#
# * http://evolution.genetics.washington.edu/phylip/newick_doc.html
# * http://www.phylosoft.org/forester/NHX.html
#
require 'strscan'
require 'bio/tree'
module Bio
class Tree
#---
# newick output
#+++
# default options
DEFAULT_OPTIONS =
{ :indent => ' ' }
def __get_option(key, options)
if (r = options[key]) != nil then
r
elsif @options && (r = @options[key]) != nil then
r
else
DEFAULT_OPTIONS[key]
end
end
private :__get_option
# formats Newick label (unquoted_label or quoted_label)
def __to_newick_format_label(str, options)
if __get_option(:parser, options) == :naive then
return str.to_s
end
str = str.to_s
if /([\(\)\,\:\[\]\_\'\x00-\x1f\x7f])/ =~ str then
# quoted_label
return "\'" + str.gsub(/\'/, "\'\'") + "\'"
end
# unquoted_label
return str.gsub(/ /, '_')
end
private :__to_newick_format_label
# formats leaf
def __to_newick_format_leaf(node, edge, options)
label = __to_newick_format_label(get_node_name(node), options)
dist = get_edge_distance_string(edge)
bs = get_node_bootstrap_string(node)
if __get_option(:branch_length_style, options) == :disabled
dist = nil
end
case __get_option(:bootstrap_style, options)
when :disabled
label + (dist ? ":#{dist}" : '')
when :molphy
label + (dist ? ":#{dist}" : '') + (bs ? "[#{bs}]" : '')
when :traditional
label + (bs ? bs : '') + (dist ? ":#{dist}" : '')
else
# default: same as molphy style
label + (dist ? ":#{dist}" : '') + (bs ? "[#{bs}]" : '')
end
end
private :__to_newick_format_leaf
# formats leaf for NHX
def __to_newick_format_leaf_NHX(node, edge, options)
label = __to_newick_format_label(get_node_name(node), options)
dist = get_edge_distance_string(edge)
bs = get_node_bootstrap_string(node)
if __get_option(:branch_length_style, options) == :disabled
dist = nil
end
nhx = {}
# bootstrap
nhx[:B] = bs if bs and !(bs.empty?)
# EC number
nhx[:E] = node.ec_number if node.instance_eval {
defined?(@ec_number) && self.ec_number
}
# scientific name
nhx[:S] = node.scientific_name if node.instance_eval {
defined?(@scientific_name) && self.scientific_name
}
# taxonomy id
nhx[:T] = node.taxonomy_id if node.instance_eval {
defined?(@taxonomy_id) && self.taxonomy_id
}
# :D (gene duplication or speciation)
if node.instance_eval { defined?(@events) && !(self.events.empty?) } then
if node.events.include?(:gene_duplication)
nhx[:D] = 'Y'
elsif node.events.include?(:speciation)
nhx[:D] = 'N'
end
end
# log likelihood
nhx[:L] = edge.log_likelihood if edge.instance_eval {
defined?(@log_likelihood) && self.log_likelihood }
# width
nhx[:W] = edge.width if edge.instance_eval {
defined?(@width) && self.width }
# merges other parameters
flag = node.instance_eval { defined? @nhx_parameters }
nhx.merge!(node.nhx_parameters) if flag
flag = edge.instance_eval { defined? @nhx_parameters }
nhx.merge!(edge.nhx_parameters) if flag
nhx_string = nhx.keys.sort{ |a,b| a.to_s <=> b.to_s }.collect do |key|
"#{key.to_s}=#{nhx[key].to_s}"
end.join(':')
nhx_string = "[&&NHX:" + nhx_string + "]" unless nhx_string.empty?
label + (dist ? ":#{dist}" : '') + nhx_string
end
private :__to_newick_format_leaf_NHX
#
def __to_newick(parents, source, depth, format_leaf,
options, &block)
result = []
if indent_string = __get_option(:indent, options) then
indent0 = indent_string * depth
indent = indent_string * (depth + 1)
newline = "\n"
else
indent0 = indent = newline = ''
end
out_edges = self.out_edges(source)
if block_given? then
out_edges.sort! { |edge1, edge2| yield(edge1[1], edge2[1]) }
else
out_edges.sort! do |edge1, edge2|
o1 = edge1[1].order_number
o2 = edge2[1].order_number
if o1 and o2 then
o1 <=> o2
else
edge1[1].name.to_s <=> edge2[1].name.to_s
end
end
end
out_edges.each do |src, tgt, edge|
if parents.include?(tgt) then
;;
elsif self.out_degree(tgt) == 1 then
result << indent + __send__(format_leaf, tgt, edge, options)
else
result <<
__to_newick([ src ].concat(parents), tgt, depth + 1,
format_leaf, options) +
__send__(format_leaf, tgt, edge, options)
end
end
indent0 + "(" + newline + result.join(',' + newline) +
(result.size > 0 ? newline : '') + indent0 + ')'
end
private :__to_newick
# Returns a newick formatted string.
# If block is given, the order of the node is sorted
# (as the same manner as Enumerable#sort).
#
# Available options:
# <tt>:indent</tt>::
# indent string; set false to disable (default: ' ')
# <tt>:bootstrap_style</tt>::
# <tt>:disabled</tt> disables bootstrap representations.
# <tt>:traditional</tt> for traditional style.
# <tt>:molphy</tt> for Molphy style (default).
def output_newick(options = {}, &block) #:yields: node1, node2
root = @root
root ||= self.nodes.first
return '();' unless root
__to_newick([], root, 0, :__to_newick_format_leaf, options, &block) +
__to_newick_format_leaf(root, Edge.new, options) +
";\n"
end
alias newick output_newick
# Returns a NHX (New Hampshire eXtended) formatted string.
# If block is given, the order of the node is sorted
# (as the same manner as Enumerable#sort).
#
# Available options:
# <tt>:indent</tt>::
# indent string; set false to disable (default: ' ')
#
def output_nhx(options = {}, &block) #:yields: node1, node2
root = @root
root ||= self.nodes.first
return '();' unless root
__to_newick([], root, 0,
:__to_newick_format_leaf_NHX, options, &block) +
__to_newick_format_leaf_NHX(root, Edge.new, options) +
";\n"
end
# Returns formatted text (or something) of the tree
# Currently supported format is: :newick, :nhx
def output(format, *arg, &block)
case format
when :newick
output_newick(*arg, &block)
when :nhx
output_nhx(*arg, &block)
when :phylip_distance_matrix
output_phylip_distance_matrix(*arg, &block)
else
raise 'Unknown format'
end
end
#---
# This method isn't suitable to written in this file?
#+++
# Generates phylip-style distance matrix as a string.
# if nodes is not given, all leaves in the tree are used.
# If the names of some of the given (or default) nodes
# are not defined or are empty, the names are automatically generated.
def output_phylip_distance_matrix(nodes = nil, options = {})
nodes = self.leaves unless nodes
names = nodes.collect do |x|
y = get_node_name(x)
y = sprintf("%x", x.__id__.abs) if y.empty?
y
end
m = self.distance_matrix(nodes)
Bio::Phylip::DistanceMatrix.generate(m, names, options)
end
end #class Tree
#---
# newick parser
#+++
# Newick standard phylogenetic tree parser class.
#
# This is alpha version. Incompatible changes may be made frequently.
class Newick
# delemiter of the entry
DELIMITER = RS = ";"
# parse error class
class ParseError < RuntimeError; end
# same as Bio::Tree::Edge
Edge = Bio::Tree::Edge
# same as Bio::Tree::Node
Node = Bio::Tree::Node
# Creates a new Newick object.
# _options_ for parsing can be set.
#
# Available options:
# <tt>:bootstrap_style</tt>::
# <tt>:traditional</tt> for traditional bootstrap style,
# <tt>:molphy</tt> for molphy style,
# <tt>:disabled</tt> to ignore bootstrap strings.
# For details of default actions, please read the notes below.
# <tt>:parser</tt>::
# <tt>:naive</tt> for using naive parser, compatible with
# BioRuby 1.1.0, which ignores quoted strings and
# do not convert underscores to spaces.
#
# Notes for bootstrap style:
# Molphy-style bootstrap values may always be parsed, even if
# the <tt>options[:bootstrap_style]</tt> is set to
# <tt>:traditional</tt> or <tt>:disabled</tt>.
#
# Note for default or traditional bootstrap style:
# By default, if all of the internal node's names are numeric
# and there are no NHX and no molphy-style boostrap values,
# the names of internal nodes are regarded as bootstrap values.
# <tt>options[:bootstrap_style] = :disabled</tt> or <tt>:molphy</tt>
# to disable the feature (or at least one NHX tag exists).
def initialize(str, options = nil)
str = str.sub(/\;(.*)/m, ';')
@original_string = str
@entry_overrun = $1
@options = (options or {})
end
# parser options
# (in some cases, options can be automatically set by the parser)
attr_reader :options
# original string before parsing
attr_reader :original_string
# string after this entry
attr_reader :entry_overrun
# Gets the tree.
# Returns a Bio::Tree object.
def tree
if !defined?(@tree)
@tree = __parse_newick(@original_string, @options)
else
@tree
end
end
# Re-parses the tree from the original string.
# Returns self.
# This method is useful after changing parser options.
def reparse
remove_instance_variable(:tree)
self.tree
self
end
private
# gets a option
def __get_option(key, options)
options[key] or (@options ? @options[key] : nil)
end
# Parses newick formatted leaf (or internal node) name.
def __parse_newick_leaf(leaf_tokens, node, edge, options)
t = leaf_tokens.shift
if !t.kind_of?(Symbol) then
node.name = t
t = leaf_tokens.shift
end
if t == :':' then
t = leaf_tokens.shift
if !t.kind_of?(Symbol) then
edge.distance_string = t if t and !(t.strip.empty?)
t = leaf_tokens.shift
end
end
if t == :'[' then
btokens = leaf_tokens
case __get_option(:original_format, options)
when :nhx
# regarded as NHX string which might be broken
__parse_nhx(btokens, node, edge)
when :traditional
# simply ignored
else
case btokens[0].to_s.strip
when ''
# not automatically determined
when /\A\&\&NHX/
# NHX string
# force to set NHX mode
@options[:original_format] = :nhx
__parse_nhx(btokens, node, edge)
else
# Molphy-style boostrap values
# let molphy mode if nothing determined
@options[:original_format] ||= :molphy
bstr = ''
while t = btokens.shift and t != :']'
bstr.concat t.to_s
end
node.bootstrap_string = bstr
end #case btokens[0]
end
end
if !btokens and !leaf_tokens.empty? then
# syntax error?
end
node.name ||= '' # compatibility for older BioRuby
# returns true
true
end
# Parses NHX (New Hampshire eXtended) string
def __parse_nhx(btokens, node, edge)
btokens.shift if btokens[0] == '&&NHX'
btokens.each do |str|
break if str == :']'
next if str.kind_of?(Symbol)
tag, val = str.split(/\=/, 2)
case tag
when 'B'
node.bootstrap_string = val
when 'D'
case val
when 'Y'
node.events.push :gene_duplication
when 'N'
node.events.push :speciation
end
when 'E'
node.ec_number = val
when 'L'
edge.log_likelihood = val.to_f
when 'S'
node.scientific_name = val
when 'T'
node.taxonomy_id = val
when 'W'
edge.width = val.to_i
when 'XB'
edge.nhx_parameters[:XB] = val
when 'O', 'SO'
node.nhx_parameters[tag.to_sym] = val.to_i
else # :Co, :SN, :Sw, :XN, and others
node.nhx_parameters[tag.to_sym] = val
end
end #each
true
end
# splits string to tokens
def __parse_newick_tokenize(str, options)
str = str.chop if str[-1..-1] == ';'
# http://evolution.genetics.washington.edu/phylip/newick_doc.html
# quoted_label ==> ' string_of_printing_characters '
# single quote in quoted_label is '' (two single quotes)
#
if __get_option(:parser, options) == :naive then
ary = str.split(/([\(\)\,\:\[\]])/)
ary.collect! { |x| x.strip!; x.empty? ? nil : x }
ary.compact!
ary.collect! do |x|
if /\A([\(\)\,\:\[\]])\z/ =~ x then
x.intern
else
x
end
end
return ary
end
tokens = []
ss = StringScanner.new(str)
while !(ss.eos?)
if ss.scan(/\s+/) then
# do nothing
elsif ss.scan(/[\(\)\,\:\[\]]/) then
# '(' or ')' or ',' or ':' or '[' or ']'
t = ss.matched
tokens.push t.intern
elsif ss.scan(/\'/) then
# quoted_label
t = ''
while true
if ss.scan(/([^\']*)\'/) then
t.concat ss[1]
if ss.scan(/\'/) then
# single quote in quoted_label
t.concat ss.matched
else
break
end
else
# incomplete quoted_label?
break
end
end #while true
unless ss.match?(/\s*[\(\)\,\:\[\]]/) or ss.match?(/\s*\z/) then
# label continues? (illegal, but try to rescue)
if ss.scan(/[^\(\)\,\:\[\]]+/) then
t.concat ss.matched.lstrip
end
end
tokens.push t
elsif ss.scan(/[^\(\)\,\:\[\]]+/) then
# unquoted_label
t = ss.matched.strip
t.gsub!(/[\r\n]/, '')
# unquoted underscore should be converted to blank
t.gsub!(/\_/, ' ')
tokens.push t unless t.empty?
else
# unquoted_label in end of string
t = ss.rest.strip
t.gsub!(/[\r\n]/, '')
# unquoted underscore should be converted to blank
t.gsub!(/\_/, ' ')
tokens.push t unless t.empty?
ss.terminate
end
end #while !(ss.eos?)
tokens
end
# get tokens for a leaf
def __parse_newick_get_tokens_for_leaf(ary)
r = []
while t = ary[0] and t != :',' and t != :')' and t != :'('
r.push ary.shift
end
r
end
# Parses newick formatted string.
def __parse_newick(str, options = {})
# initializing
root = Node.new
cur_node = root
edges = []
nodes = [ root ]
internal_nodes = []
node_stack = []
# preparation of tokens
ary = __parse_newick_tokenize(str, options)
previous_token = nil
# main loop
while token = ary.shift
#p token
case token
when :','
if previous_token == :',' or previous_token == :'(' then
# there is a leaf whose name is empty.
ary.unshift(token)
ary.unshift('')
token = nil
end
when :'('
node = Node.new
nodes << node
internal_nodes << node
node_stack.push(cur_node)
cur_node = node
when :')'
if previous_token == :',' or previous_token == :'(' then
# there is a leaf whose name is empty.
ary.unshift(token)
ary.unshift('')
token = nil
else
edge = Edge.new
leaf_tokens = __parse_newick_get_tokens_for_leaf(ary)
token = nil
if leaf_tokens.size > 0 then
__parse_newick_leaf(leaf_tokens, cur_node, edge, options)
end
parent = node_stack.pop
raise ParseError, 'unmatched parentheses' unless parent
edges << Bio::Relation.new(parent, cur_node, edge)
cur_node = parent
end
else
leaf = Node.new
edge = Edge.new
ary.unshift(token)
leaf_tokens = __parse_newick_get_tokens_for_leaf(ary)
token = nil
__parse_newick_leaf(leaf_tokens, leaf, edge, options)
nodes << leaf
edges << Bio::Relation.new(cur_node, leaf, edge)
end #case
previous_token = token
end #while
raise ParseError, 'unmatched parentheses' unless node_stack.empty?
bsopt = __get_option(:bootstrap_style, options)
ofmt = __get_option(:original_format, options)
unless bsopt == :disabled or bsopt == :molphy or
ofmt == :nhx or ofmt == :molphy then
# If all of the internal node's names are numeric,
# the names are regarded as bootstrap values.
flag = false
internal_nodes.each do |inode|
if inode.name and !inode.name.to_s.strip.empty? then
if /\A[\+\-]?\d*\.?\d*\z/ =~ inode.name
flag = true
else
flag = false
break
end
end
end
if flag then
@options[:bootstrap_style] = :traditional
@options[:original_format] = :traditional
internal_nodes.each do |inode|
if inode.name then
inode.bootstrap_string = inode.name
inode.name = nil
end
end
end
end
# Sets nodes order numbers
nodes.each_with_index do |xnode, i|
xnode.order_number = i
end
# If the root implicitly prepared by the program is a leaf and
# there are no additional information for the edge from the root to
# the first internal node, the root is removed.
if rel = edges[-1] and rel.node == [ root, internal_nodes[0] ] and
rel.relation.instance_eval {
!defined?(@distance) and !defined?(@log_likelihood) and
!defined?(@width) and !defined?(@nhx_parameters) } and
edges.find_all { |x| x.node.include?(root) }.size == 1
nodes.shift
edges.pop
end
# Let the tree into instance variables
tree = Bio::Tree.new
tree.instance_eval {
@pathway.relations.concat(edges)
@pathway.to_list
}
tree.root = nodes[0]
tree.options.update(@options)
tree
end
end #class Newick
end #module Bio