rbbt-entities 0.1.0

data/LICENSE

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+Copyright (c) 2010-2011 Miguel Vázquez García
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/lib/rbbt/entity/gene.rb

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+require 'rbbt/entity'
+require 'rbbt/workflow'
+require 'rbbt/sources/organism'
+require 'rbbt/sources/entrez'
+
+Workflow.require_workflow "Translation"
+
+module Gene
+  extend Entity
+
+  self.annotation :format
+  self.annotation :organism
+
+  self.format = Organism::Hsa.identifiers.all_fields
+
+  def name
+    to "Associated Gene Name"
+  end
+
+  def description
+    if Array === self
+      to("Entrez Gene ID").collect{|id| gene = Entrez.get_gene(id); gene.nil? ? nil : gene.summary}
+    else
+      gene = Entrez.get_gene(to("Entrez Gene ID"))
+      gene.nil? ? nil : gene.summary
+    end
+  end
+
+  def to!(new_format)
+    if Array === self
+      Gene.setup(Translation.job(:tsv_translate, "", :organism => organism, :genes => self, :format => new_format).exec.values_at(*self), new_format, organism)
+    else
+      Gene.setup(Translation.job(:tsv_translate, "", :organism => organism, :genes => [self], :format => new_format).exec[self], new_format, organism)
+    end
+  end
+
+  def to(new_format)
+    return self if format == new_format
+    if Array === self
+      to!(new_format).collect!{|v| v.nil? ? nil : v.first}
+    else
+      v = to!(new_format)
+      v.nil? ? nil : v.first
+    end
+  end
+
+  def self2pfam
+    index = Organism.gene_pfam(organism).tsv :type => :flat, :persist => true
+    if Array === self
+      index.values_at(*self).flatten
+    else
+      index[self]
+    end
+  end
+
+  def chromosome
+    chr = Organism.gene_positions(organism).tsv :fields => ["Chromosome Name"], :type => :single, :persist => true
+    if Array === self
+      to("Ensembl Gene ID").collect do |gene|
+        chr[gene]
+      end
+    else
+      chr[to("Ensembl Gene ID")]
+    end
+  end
+
+  def range
+    pos = Organism.gene_positions(organism).tsv :fields => ["Gene Start", "Gene End"], :type => :list, :persist => true, :cast => :to_i
+    if Array === self
+      to("Ensembl Gene ID").collect do |gene|
+        next if not pos.include? gene
+        Range.new *pos[gene]
+      end
+    else
+      return nil if not pos.include? to("Ensembl Gene ID")
+      Range.new *pos[to("Ensembl Gene ID")]
+    end
+  end
+
+end
+
+module Transcript
+  extend Entity
+
+  def to!(new_format)
+    if Array === self
+      Gene.setup(Translation.job(:tsv_probe_translate, "", :organism => organism, :genes => self, :format => new_format).exec.values_at(*self), new_format, organism)
+    else
+      Gene.setup(Translation.job(:tsv_probe_translate, "", :organism => organism, :genes => [self], :format => new_format).exec[self], new_format, organism)
+    end
+  end
+
+  def to(new_format)
+    return self if format == new_format
+    if Array === self
+      to!(new_format).collect{|v| v.nil? ? nil : v.first}
+    else
+      v = to!(new_format)
+      v.nil? ? nil : v.first
+    end
+  end
+end

data/lib/rbbt/entity/genotype.rb

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+require 'rbbt/entity'
+require 'rbbt/workflow'
+require 'rbbt/sources/organism'
+require 'rbbt/mutation/mutation_assessor'
+require 'rbbt/entity/protein'
+
+Workflow.require_workflow "Sequence"
+
+module MutatedIsoform
+  extend Entity
+  self.annotation :organism
+
+  self.format = "Mutated Isoform"
+
+  def protein
+    if Array === self
+      Protein.setup(self.collect{|mutation| mutation.split(":").first}, "Ensembl Protein ID", organism)
+    else
+      Protein.setup(self.split(":").first, "Ensembl Protein ID", organism)
+    end
+  end
+
+  def ensembl_protein_image_url
+    if Array === self
+      self.collect{|e| e.ensembl_protein_image_url}
+    else
+      ensembl_url = if organism == "Hsa" then "www.ensembl.org" else "#{organism.sub(/.*\//,'')}.archive.ensembl.org" end
+      "http://#{ensembl_url}/Homo_sapiens/Component/Transcript/Web/TranslationImage?db=core;p=#{protein};_rmd=d2a8;export=svg"
+    end
+  end
+
+  ASTERISK = "*"[0]
+  def single_type
+    prot, change = self.split(":")
+
+    case
+    when change =~ /UTR/
+      "UTR"
+    when (change[0] == ASTERISK and not change[0] == change[-1])
+      "NOSTOP"
+    when (change[-1] == ASTERISK and not change[0] == change[-1])
+      "NONSENSE"
+    when change =~ /Indel/
+      "INDEL"
+    when change =~ /FrameShift/
+      "FRAMESHIFT"
+    when change[0] == change[-1]
+      "SYNONYMOUS"
+    else
+      "MISS-SENSE"
+    end
+  end
+
+  def ary_type
+    self.collect{|mutation| mutation.single_type}
+  end
+
+
+  def type
+    Array === self ? ary_type : single_type
+  end
+
+  def filter(*types)
+    list = self.zip(type).select do |mutation, type|
+      types.include? type
+    end.collect{|mutation, type| mutation}
+
+    MutatedIsoform.setup(list, organism)
+  end
+
+  def self2mutation_assessor_prediction
+    if Array === self
+      filtered = filter "MISS-SENSE"
+      correspondance = {}
+      mutations = filtered.zip(filtered.protein.to "UniProt/SwissProt ID").collect do |mutation, uniprot|
+        prot, change = mutation.split(":")
+        next if uniprot.nil?
+        uniprot_change = [uniprot, change]
+        correspondance[uniprot_change] = mutation
+        uniprot_change
+      end.compact
+
+      tsv = MutationAssessor.chunked_predict(mutations)
+      return TSV.setup({}, :key_field => "Mutated Isoform", :fields => ["Func. Impact"]) if tsv.empty?
+      tsv.add_field "Mutated Isoform" do |key, values|
+        correspondance[key.split(" ")]
+      end
+      tsv.reorder "Mutated Isoform", ["Func. Impact"]
+    else
+      prot, change = mutation.split(":")
+      uniprot = protein.to "UniProt/SwissProt ID"
+      mutations = [uniprot, change]
+
+      tsv = MutationAssessor.chunked_predict(mutations)
+      tsv.add_field "Mutated Isoform" do |key, values|
+        self
+      end
+      tsv.reorder "Mutated Isoform", ["Func. Impact"]
+    end
+  end
+
+  def early_nonsense
+    protein_sequences = Organism.protein_sequence(organism).tsv :persist => true, :type => :single
+    filter("NONSENSE").select{|isoform_mutation|
+      protein, mutation = isoform_mutation.split ":"
+      if protein_sequences.include? protein
+        mutation.match(/(\d+)/)[1].to_f < protein_sequences[protein].length.to_f * 0.7
+      else
+        false
+      end
+    }
+  end
+
+  def early_frameshifts
+    protein_sequences = Organism.protein_sequence(organism).tsv :persist => true, :type => :single
+    filter("FRAMESHIFT").select{|isoform_mutation|
+      protein, mutation = isoform_mutation.split ":"
+      if protein_sequences.include? protein
+        mutation.match(/(\d+)/)[1].to_f < protein_sequences[protein].length.to_f * 0.7
+      else
+        false
+      end
+    }
+  end
+
+  def damaged(options = {})
+    options = Misc.add_defaults options, :mutation_assesor_cutoff => :medium, :non_sense => true, :frameshift => true
+
+    levels = [:low, :medium, :high].collect{|v| v.to_s}
+    cutoff = levels.index options[:mutation_assesor_cutoff].to_s
+
+    predicted = self2mutation_assessor_prediction.select{|k, v| 
+      if v.nil?
+        false
+      else
+        value = levels.index(v[0].to_s)
+        value and value >= cutoff
+      end
+    }.collect{|k,v| k}
+
+    predicted += early_nonsense if options[:non_sense]
+    predicted += early_frameshifts if options[:frameshift]
+
+    MutatedIsoform.setup(predicted, organism)
+  end
+end
+
+module GenomicMutation
+  extend Entity
+  self.annotation :name
+  self.annotation :organism
+
+  self.format = "Genomic Mutation"
+
+  def self2genes
+    Sequence.job(:genes_at_genomic_positions, name, :organism => organism, :positions => Array === self ? self : [self]).run
+  end
+
+  def genes
+    Gene.setup(self2genes.values.flatten.uniq, "Ensembl Gene ID", organism)
+  end
+
+  def self2mutated_isoforms
+    Sequence.job(:mutated_isoforms_for_genomic_mutations, name, :organism => organism, :mutations => Array === self ? self : [self]).run
+  end
+
+  def mutated_isoforms
+    MutatedIsoform.setup(self2mutated_isoforms.values.flatten, organism)
+  end
+
+  def damaging_mutations(options = {})
+    damaged_isoforms = mutated_isoforms.damaged(options)
+    damaging_mutations = self2mutated_isoforms.select{|mutation, values|
+      mutated_isoforms = values["Mutated Isoform"]
+      (damaged_isoforms & mutated_isoforms).any?
+    }.collect{|mutation, mutated_isoforms| mutation.dup}
+    GenomicMutation.setup(damaging_mutations, name + '.damaging', organism)
+  end
+
+  def mutations_at_genes(genes)
+    genes = genes.to("Ensembl Gene ID").compact
+    s2g = self.self2genes 
+    subset = s2g.select("Ensembl Gene ID" => genes).keys.collect{|e| e.dup}
+    GenomicMutation.setup(subset, name + '.mutations_at_genes', organism)
+  end
+end

data/lib/rbbt/entity/misc.rb

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+require 'rbbt/entity'
+require 'rbbt/workflow'
+require 'rbbt/sources/go'
+require 'rbbt/sources/organism'
+require 'rbbt/entity/gene'
+
+module GOTerm
+  extend Entity
+  self.annotation :organism
+
+  self.format = ["GO Term", "GO ID"]
+
+  def name
+    if Array === self
+      self.collect{|id| GO.id2name(id)}
+    else
+      GO.id2name(self)
+    end
+  end
+
+  def genes
+    go2genes = Organism.gene_go(organism).tsv(:key_field => "GO ID", :fields => ["Ensembl Gene ID"], :merge => true, :persist => true)
+    go2genes.unnamed = true
+    Gene.setup(go2genes[self].first, "Ensembl Gene ID", organism)
+  end
+end

data/lib/rbbt/entity/protein.rb

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+require 'rbbt/entity'
+require 'rbbt/workflow'
+require 'rbbt/sources/organism'
+require 'rbbt/statistics/hypergeometric'
+require 'rbbt/network/paths'
+
+Workflow.require_workflow "Translation"
+
+module Protein
+  extend Entity
+  include Entity::Adjacent
+  include Entity::Enriched
+
+  self.annotation :format
+  self.annotation :organism
+
+  def gene
+    Gene.setup(to("Ensembl Protein ID"), "Ensembl Protein ID", organism)
+  end
+
+  def to(new_format)
+    return self if format == new_format
+    if Array === self
+      Protein.setup(Translation.job(:translate_protein, "", :organism => organism, :proteins => self, :format => new_format).exec, new_format, organism)
+    else
+      Protein.setup(Translation.job(:translate_protein, "", :organism => organism, :proteins => [self], :format => new_format).exec.first, new_format, organism)
+    end
+  end
+end
+

data/lib/rbbt/entity.rb

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+require 'rbbt/annotations'
+
+module Entity
+  class << self
+    attr_accessor :formats
+  end
+  self.formats = {}
+  
+  def self.extended(base)
+    base.extend Annotation unless Annotation === base
+
+    Entity.formats[base.to_s] = base
+    base.module_eval do
+      class << self
+        attr_accessor :template
+        alias prev_entity_extended extended
+      end
+
+      def self.extended(data)
+        prev_entity_extended(data)
+        data.extend AnnotatedArray
+      end
+
+      def self.format=(formats)
+        formats = [formats] unless Array === formats
+        formats.each do |format|
+          Entity.formats[format] = self
+        end
+      end
+    end
+  end
+end
+

data/test/rbbt/entity/test_gene.rb

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+require File.expand_path(File.dirname(__FILE__) + '/../../test_helper')
+
+require 'test/unit'
+require 'rbbt/util/tmpfile'
+require 'test/unit'
+require 'rbbt/entity/gene'
+
+class TestGene < Test::Unit::TestCase
+  def test_to
+    assert_equal "1020", Gene.setup("CDK5", "Associated Gene Name", "Hsa").to("Entrez Gene ID")
+  end
+end
+
+

data/test/test_helper.rb

@@ -0,0 +1,4 @@
+require 'test/unit'
+$LOAD_PATH.unshift(File.expand_path(File.join(File.dirname(__FILE__), '..', 'lib')))
+$LOAD_PATH.unshift(File.expand_path(File.dirname(__FILE__)))
+

metadata

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+--- !ruby/object:Gem::Specification 
+name: rbbt-entities
+version: !ruby/object:Gem::Version 
+  hash: 27
+  prerelease: 
+  segments: 
+  - 0
+  - 1
+  - 0
+  version: 0.1.0
+platform: ruby
+authors: 
+- Miguel Vazquez
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2011-10-03 00:00:00 +02:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: rbbt-util
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  type: :runtime
+  version_requirements: *id001
+- !ruby/object:Gem::Dependency 
+  name: rbbt-sources
+  prerelease: false
+  requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  type: :runtime
+  version_requirements: *id002
+- !ruby/object:Gem::Dependency 
+  name: rbbt-dm
+  prerelease: false
+  requirement: &id003 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  type: :runtime
+  version_requirements: *id003
+description: Entities for handling tsv files, caches, etc
+email: miguel.vazquez@cnio.es
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- LICENSE
+files: 
+- LICENSE
+- lib/rbbt/entity.rb
+- lib/rbbt/entity/gene.rb
+- lib/rbbt/entity/genotype.rb
+- lib/rbbt/entity/misc.rb
+- lib/rbbt/entity/protein.rb
+- test/test_helper.rb
+- test/rbbt/entity/test_gene.rb
+has_rdoc: true
+homepage: http://github.com/mikisvaz/rbbt-util
+licenses: []
+
+post_install_message: 
+rdoc_options: []
+
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.6.2
+signing_key: 
+specification_version: 3
+summary: Entities for the Ruby Bioinformatics Toolkit (rbbt)
+test_files: 
+- test/test_helper.rb
+- test/rbbt/entity/test_gene.rb