bio-nexml is listed at http://biogems.info/
NeXML is a file format for phylogenetic data. It is inspired by the modular architecture of the commonly-used NEXUS file format (hence the name) in that a NeXML instance document can contain:
The elements in a NeXML document can be annotated using RDFa (http://en.wikipedia.org/wiki/RDFa), which means that every object that can be parsed out of a NeXML document must be an object that, in turn, can be annotated with predicates (and their namespaces) and other objects (with, perhaps, their own namespaces). The advantage over previous file formats is that we can retain all metadata for all objects within one file, regardless where the metadata come from.
NeXML can be transformed to RDF using an XSL stylesheet. As such, NeXML forms an intermediate format between traditional flat file formats (with predictable structure but no semantics) and RDF (with loose structure, but lots of semantics) that is both easy to work with, yet ready for the Semantic Web.
To learn more, visit http://www.nexml.org
Currently all the parsing is done at the start( i.e. no streaming ). This is likely to change later. Parse an NeXML file:
doc = Bio::NeXML::Parser.new( "trees.xml" )
nexml = doc.parse
nexml.class #Bio::NeXML::Nexml
Bio::NeXML::Writer
class provides a wrapper over libxml-ruby to create any NeXML document. This class defines a set of serialize_*
instance methods which can be called on the appropriate object to get its NeXML representation. The method returns a XML::Node
object. To get the raw NeXML representation to_s
method should be called on the return value.
NeXML defines three top level containers: otus
, trees
, characters
which bear parent-child relation with other NeXML elements. In effect, a valid NeXML document has only three type of immediate children. Naturally, a typical working paradigm would be to create Bio::NeXML::Otus
, Bio::NeXML::Trees
, and Bio::NeXML::Characters
objects and write them to the NeXML file.
# Parse a test file. This will give us Bio::NeXML::Otus,
# Bio::NeXML::Trees, and Bio::NeXML::Characters object.
doc1 = Bio::NeXML::Parser.new 'test.xml'
nexml = doc1.parse
doc1.close
# Create a Writer object,
writer = Bio::NeXML::Writer.new
# add otus, trees and characters to it,
writer << nexml.otus
writer << nexml.trees
writer << nexml.characters
# save it.
writer.save 'sample.xml'
Bio::NeXML::Writer
internally calls some serialize_*
method at the lowest level. If need be, these serialize_*
methods can be called to obtain raw NeXML representation of any NeXML element.
# Create an otus object with a child otu element
taxa1 = Bio::NeXML::Otus.new 'taxa1', 'A taxa block'
o1 = Bio::NeXML::Otu.new 'o1', 'A taxon'
taxa1 << o1
# Obtain the raw NeXML representation of the otus object created
writer = Bio::NeXML::Writer.new
writer.serialize_otus( taxa1 ).to_s
# => "<otus label=\"A taxa block\" id=\"taxa1\">\n <otu label=\"A taxon\" id=\"o1\"/>\n</otus>"
Unit tests for serializer are filled with such use cases.
#get a hash of otus objects indexed with 'id'
nexml.otus_set
#get an array of otus objects
nexml.otus
#get an otus by id
taxa1 = nexml.get_otus_by_id "taxa1"
#iterate over each otus object
nexml.each_otus do |taxa|
puts taxa.id
puts taxa.label
end
#characters
nexml.trees_set #return a hash of trees object indexed with 'id'
nexml.trees #return an array of trees objects.
#iterate over each trees object
nexml.each_trees do |trees|
puts trees.id
puts trees.label
end
#find a trees by id
trees1 = nexml.get_trees_by_id 'trees1'
# characters
nexml.characters_set #return a hash of characters object indexed with 'id'
nexml.characters #return an array of characters object
#iterate over each characters object
nexml.each_characters do |ch|
puts ch.id
puts ch.label
end
#find a characters object by id
characters = nexml.get_characters_by_id 'chars1'
Taxa blocks and taxons are stored internally as a Ruby hash for faster 'id' based lookup. Consider [https://www.nescent.org/wg_phyloinformatics/NeXML_Elements#Example this] NeXML snippet
#get the id of otus
taxa1.id # "taxa1"
#get the label of otus
taxa1.label # "Primary taxa block"
#get a hash of child otu objects indexed with id
taxa1.otu_set
#get an array of child otu objects
taxa1.otus
#get an otu object by id
#get_otu_by_id is an alias of []
t1 = taxa1[ 't1' ]
#add an otu object to otus
t1.add_otu( otu_object )
#to add more than one otu object at a time use << or otus= method
t1 << [otu_object1, otu_object2]
t1.otus = otu_object1, otu_object2
#or iterate over each otu object
#each_otu is an alias for each
taxa1.each do |taxon|
puts taxon.id
puts taxon.label
end
#check if an otu with given id belongs to an otus or not
#include? and has? are alias for has_otu?
taxa1.has_otu? 't2' # => true
taxa1.has? 't8' # => false
#an otus object in enumerable
taxa1.map &:id # => array of otu ids
taxa1.select {|t| t.class == "Lemurs" } #maybe in future
#get an otu's id
t1.id # => "t1"
#get an otu's label
t1.label # => "Homo sapiens"
Trees and tree and network are stored internally as a Ruby hash for faster 'id' based lookup.
trees1.class #Bio::NeXML::Trees
#get the taxa block to which the trees is linked to
trees1.otus #returns an otus object
trees1.tree_set #return a hash or tree objects indexed with 'id'
tress1.trees #return an arrayof trees object
#iterate over each tree object
trees1.each_tree do |t|
puts t.id
puts t.label
end
#get a tree object with its 'tree1'
tree1 = trees1[ 'tree1' ]
#or, with a conventional method call
tree1 = trees1.get_tree_by_id 'tree1'
#or, from a nexml object
tree1 = nexml.get_tree_by_id 'tree1'
tree1.class #Bio::NeXML::IntTree or Bio::NeXML::FloatTree
#check if a tree belongs to a trees or not
#pass it a tree id
tree1.has_tree? 'tree1' #return true or false
#get the number of treess
trees1.number_of_trees
trees1.network_set #return a hash or network objects indexed with 'id'
tress1.networks #return an arrayof network objects
#iterate over each network object
trees1.each_network do |n|
puts n.id
puts n.label
end
#get a network object with its id
network1 = trees1[ 'network1' ]
#or, with a conventional method call
network1 = trees1.get_network_by_id 'network1'
#or, from a nexml object
network1 = nexml.get_tree_by_id 'network1'
network1.class #Bio::NeXML::IntTree or Bio::NeXML::FloatTree
#check if a network belongs to a trees or not
#pass it a network id
trees1.has_network? 'network1' #return true or false
#get the number of networks
trees1.number_of_networks
#iterate over both trees and networks
trees1.each do |g|
puts g.class
end
#find if a tree or a network belongs to a trees or not
#include? is an alias for has?
trees1.has? 'tree1' #return true or false
#total number of trees and networks
trees1.number_of_graphs
All the available methods from [http://bioruby.org/rdoc/classes/Bio/Tree.html#M001688 Bio::Tree] class can be called on a tree object.
node1 = tree.get_node_by_name "n3" #note name is same as id
tree1.parents node1
A trees object is an enumerable:
trees1.map &:id
puts characters.class
#get the taxa block to which the characters is linked to
characters.otus #returns an otus object
#get the child format element
format = characters.format
puts format.class
#get the child matrix element
matrix = characters.matrix
puts matrix.class
format.states_set #return a hash of states objects indexed with 'id'
format.states #return an array of states object
#iterate over each states object
format.each_states do |states|
puts states.id
puts states.label
end
#get a states object by id
states = format.get_states_by_id 'states1'
#check if the states object with 'id' belongs to format or not
format.has_states? 'states1'
format.char_set #return a hash of char objects indexed with 'id'
format.chars #return an array of char objects
#iterate over each char object
format.each_char do |char|
puts char.id
puts char.label
end
#get a char object by id
char = format.get_char_by_id 'char1'
#check if the char object with 'id' belongs to format or not
format.has_char? 'char1'
#get a states or a char object by id
state = format[ 'states1' ]
char = format[ 'char1' ]
#check if a states or a char object with 'id' belongs to format or not
format.has? 'states1'
format.has? 'char1'
#all objects, including char and states can be iterated over with each
format.each do |obj|
puts obj.class
end
#format is enumerable
format.map &:id
states.state_set #return a hash of state objects indexed with 'id'
states.states #return an array of state objects
#iterate over each state object
states.each_state do |state|
puts state.id
end
#or, use its alias each
#get a state object by id
state = states.get_state_by_id 'state1'
#or, use hash notation
state = states[ 'state1' ]
#check if a state belongs to states or not
states.has_state? 'state1'
#or, use its alias has? and include?
#get the symbol associated with the state
state.symbol
#find if the state is ambiguous
state.ambiguous?
#find the kind of ambiguity
state.ambiguity
#find if it is an uncertain state set
state.uncertain?
#find if it is a polymorphic state set
state.polymorphic?
#get the members of a state set as an array
state.members
#or iterate over each member
state.each do |member|
puts member.class #same as self
puts member.id
end
#a state is Enumerable over its members
state.select{ |member| member.id == "rna5" }
#get the id
char.id
#get the label
char.label
#get the states object the char is linked to
char.states
#get the codon position for DnaChar and RnaChar objects
char.codon
...
The research leading to these results has received funding from the [European Community's] Seventh Framework Programme ([FP7/2007-2013] under grant agreement n¡ [237046].
If you use this software, please cite:
NeXML: rich, extensible, and verifiable representation of comparative data and metadata
and
Copyright (c) 2011 Rutger Vos and Anurag Priyam. See LICENSE.txt for further details.