Class: Bio::PhyloXML::Sequence

Inherits:
Object
  • Object
show all
Defined in:
lib/bio-phyloxml/phyloxml_elements.rb

Overview

Description

Element Sequence is used to represent a molecular sequence (Protein, DNA, RNA) associated with a node.

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize ⇒ Sequence

Returns a new instance of Sequence.



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 551

def initialize
  @annotations = []
  @other = []
end

Instance Attribute Details

#accession ⇒ Object

Accession object. Holds source and identifier for the sequence.



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 528

def accession
  @accession
end

#annotations ⇒ Object

Array of Annotation objects. Annotations of molecular sequence.



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 543

def annotations
  @annotations
end

#domain_architecture ⇒ Object

DomainArchitecture object. Describes domain architecture of a protein.



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 545

def domain_architecture
  @domain_architecture
end

#id_ref ⇒ Object

String. One intended use for ‘id_ref’ is to link a sequence to a taxonomy (via the taxonomy’s ‘id_source’) in the case of multiple sequences and taxonomies per node.



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 523

def id_ref
  @id_ref
end

#id_source ⇒ Object

String. Used to link with other elements.



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 519

def id_source
  @id_source
end

#is_aligned ⇒ Object

Boolean. used to indicated that this molecular sequence is aligned with all other sequences in the same phylogeny for which ‘is aligned’ is true as well (which, in most cases, means that gaps were introduced, and that all sequences for which ‘is aligned’ is true must have the same length)



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 538

def is_aligned
  @is_aligned
end

#location ⇒ Object

String. Location of a sequence on a genome/chromosome



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 530

def location
  @location
end

#mol_seq ⇒ Object

String. The actual sequence is stored here.



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 532

def mol_seq
  @mol_seq
end

#name ⇒ Object

Full name (e.g. muscle Actin )



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 516

def name
  @name
end

#other ⇒ Object

Array of Other objects. Used to save additional information from other than PhyloXML namspace.



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 549

def other
  @other
end

#symbol ⇒ Object

short (maximal ten characters) symbol of the sequence (e.g. ‘ACTM’)



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 526

def symbol
  @symbol
end

#type ⇒ Object

Type of sequence (rna, dna, protein)



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 513

def type
  @type
end

#uri ⇒ Object

Uri object



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 541

def uri
  @uri
end

Instance Method Details

#is_aligned? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 566

def is_aligned?
  @is_aligned
end

#to_biosequence ⇒ Object

converts Bio::PhyloXML:Sequence to Bio::Sequence object.

Returns

Bio::Sequence



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 617

def to_biosequence
  #type is not a required attribute in phyloxml (nor any other Sequence
  #element) it might not hold any value, so we will not check what type it is.
  seq = Bio::Sequence.auto(@mol_seq)

  seq.id_namespace = @accession.source
  seq.entry_id = @accession.value
  # seq.primary_accession = @accession.value could be this
  seq.definition = @name
  #seq.comments = @name //this one?
  if (defined? @uri) && @uri
    h = {'url' => @uri.uri,
      'title' => @uri.desc }
    ref = Bio::Reference.new(h)
    seq.references << ref
  end
  seq.molecule_type = 'RNA' if @type == 'rna'
  seq.molecule_type = 'DNA' if @type == 'dna'

  #@todo deal with the properties. There might be properties which look
  #like bio sequence attributes or features
  return seq
end

#to_xml ⇒ Object

Converts elements to xml representation. Called by PhyloXML::Writer class.



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 579

def to_xml
  
  seq = LibXML::XML::Node.new('sequence')
  if (defined? @type) && @type
    if ["dna", "rna", "protein"].include?(@type)
      seq["type"] = @type
    else 
      raise "Type attribute of Sequence has to be one of dna, rna or a."
    end
  end
  
  PhyloXML::Writer.generate_xml(seq, self, [
      [:attr, 'id_source'],
      [:attr, 'id_ref'],
      [:pattern, 'symbol', (defined? @symbol) ? @symbol : nil, Regexp.new("^\\S{1,10}$")],
      [:complex, 'accession', (defined? @accession) ? @accession : nil],
      [:simple, 'name', (defined? @name) ? @name : nil],
      [:simple, 'location', (defined? @location) ? @location : nil]])

  if (defined? @mol_seq) && @mol_seq
    molseq = LibXML::XML::Node.new('mol_seq', @mol_seq)
    molseq["is_aligned"] = @is_aligned.to_s if (defined? @is_aligned) && @is_aligned != nil
    seq << molseq
  end

  PhyloXML::Writer.generate_xml(seq, self, [
      #[:pattern, 'mol_seq', @mol_seq, Regexp.new("^[a-zA-Z\.\-\?\*_]+$")],
      [:complex, 'uri', (defined? @uri) ? @uri : nil],
      [:objarr, 'annotation', 'annotations'],
      [:complex, 'domain_architecture', (defined? @domain_architecture) ? @domain_architecture : nil]])
      #@todo test domain_architecture
  #any
  return seq
end