rbbt-entities 1.0.0 → 1.1.0

data/lib/rbbt/entity/protein.rb

@@ -17,28 +17,61 @@ module Protein
 
   self.format = "Ensembl Protein ID"
 
-  def ensembl
+  def self.ensp2sequence(organism, protein)
+    @@ensp2sequence ||= {}
+    @@ensp2sequence[organism] ||= Organism.protein_sequence(organism).tsv :persist => true
+    if Array === protein
+      @@ensp2sequence[organism].values_at *protein
+    else
+      @@ensp2sequence[organism][protein]
+    end
+  end
+
+  def self.ensp2enst(organism, protein)
+    @@ensp2enst ||= {}
+    @@ensp2enst[organism] ||= Organism.transcripts(organism).tsv(:type => :single, :key_field => "Ensembl Protein ID", :fields => ["Ensembl Transcript ID"], :persist => true)
+    @@ensp2enst[organism][protein]
+  end
+
+  property :uniprot => :array2single do
+    to "UniProt/SwissProt Accession"
+  end
+  persist :uniprot
+
+  property :ensembl => :array2single do
     to "Ensembl Protein ID"
   end
+  persist :ensembl
+
+  property :transcript => :array2single do
+    ensembl.collect{|ensp|
+      Protein.ensp2enst(organism, ensp)
+    }
+  end
+  persist :transcript
 
   property :ensembl_protein_image_url => :single2array do
     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=#{ensembl};_rmd=d2a8;export=svg"
   end
+  persist :ensembl_protein_image_url
 
   property :to! => :array2single do |new_format|
     return self if format == new_format
     Protein.setup(Translation.job(:translate_protein, "", :organism => organism, :proteins => self, :format => new_format).exec, new_format, organism)
   end
+  persist :to!
 
   property :to => :array2single do |new_format|
     return self if format == new_format
     to!(new_format).collect!{|v| v.nil? ? nil : v.first}
   end
+  persist :to
 
-  property :gene do
+  property :gene => :array do
     Gene.setup(to("Ensembl Protein ID").clean_annotations, "Ensembl Protein ID", organism)
   end
+  persist :gene
 
   property :pfam => :array2single do
     index = Organism.gene_pfam(organism).tsv :flat, :persist => true
@@ -46,17 +79,16 @@ module Protein
     pfam = index.values_at(*self).flatten
     Pfam.setup pfam
   end
+  persist :pfam
 
   property :sequence => :array2single do
-    @protein_sequence ||= begin
-                            protein_sequence = Organism.protein_sequence(organism).tsv :persist => true
-                            protein_sequence.unnamed = true
-                            protein_sequence.values_at(*self.ensembl)
-                          end
+    Protein.ensp2sequence(organism, self.ensembl)
   end
+  persist :sequence
 
   property :sequence_length => :array2single do
     sequence.collect{|seq| seq.nil? ? nil : seq.length}
   end
+  persist :sequence_length
 end
 

data/lib/rbbt/entity/transcript.rb

@@ -0,0 +1,69 @@
+require 'rbbt/entity'
+require 'rbbt/entity/gene'
+
+module Transcript
+  extend Entity
+
+  self.annotation :format
+  self.annotation :organism
+
+  self.format = "Ensembl Transcript ID"
+
+  def self.enst2ensg(organism, transcript)
+    @@enst2ensg ||= {}
+    @@enst2ensg[organism] ||= Organism.gene_transcripts(organism).tsv(:type => :single, :key_field => "Ensembl Transcript ID", :fields => ["Ensembl Gene ID"], :persist => true).tap{|o| o.unnamed = true}
+    res = if Array === transcript
+            @@enst2ensg[organism].values_at *transcript
+          else
+            @@enst2ensg[organism][transcript]
+          end
+    Gene.setup(res, "Ensembl Gene ID", organism)
+  end
+
+  def self.enst2ensp(organism, transcript)
+    @@enst2ensp ||= {}
+    @@enst2ensp[organism] ||= Organism.transcripts(organism).tsv(:type => :single, :key_field => "Ensembl Transcript ID", :fields => ["Ensembl Protein ID"], :persist => true)
+    res = if Array === transcript
+            @@enst2ensp[organism].values_at *transcript
+          else
+            @@enst2ensp[organism][transcript]
+          end
+    Protein.setup(res, "Ensembl Protein ID", organism)
+  end
+
+
+  property :to! => :array2single do |new_format|
+    return self if format == new_format
+    Gene.setup(Translation.job(:tsv_translate_probe, "", :organism => organism, :probes => self, :format => new_format).exec.values_at(*self), new_format, organism)
+  end
+
+  property :to => :array2single do |new_format|
+    return self if format == new_format
+    to!(new_format).collect!{|v| v.nil? ? nil : v.first}
+  end
+
+  property :ensembl => :array2single do
+    to "Ensembl Transcript ID"
+  end
+
+  property :sequence => :array2single do
+    transcript_sequence = Organism.transcript_sequence(organism).tsv :persist => true
+    transcript_sequence.unnamed = true
+    transcript_sequence.values_at *self.ensembl
+  end
+
+  property :sequence_length => :array2single do
+    sequence.collect{|s|
+      s.nil? ? nil : s.length
+    }
+  end
+
+  property :gene => :array2single do
+    Transcript.enst2ensg(organism, self)
+  end
+
+  property :protein => :array2single do
+    Transcript.enst2ensp(organism, self)
+  end
+end
+

data/test/rbbt/entity/test_gene.rb

@@ -24,7 +24,7 @@ class TestGene < Test::Unit::TestCase
   def test_transcripts
     assert CDK5.transcripts.length > 1
     assert_equal "Hsa", CDK5.transcripts.organism
-    assert_equal "Hsa", CDK5.make_list.transcripts.first.organism
+    assert_equal "Hsa", CDK5.make_list.transcripts[0].organism
     assert_equal "Hsa", CDK5.transcripts.make_list.organism
   end
 

data/test/rbbt/entity/test_genomic_mutation.rb

@@ -8,15 +8,6 @@ require 'rbbt/entity/genomic_mutation'
 class TestGenomicMutation < Test::Unit::TestCase
   MUTATION = GenomicMutation.setup("10:124745844:A:158", "Test", "Hsa/jun2011")
   SPLICING = GenomicMutation.setup("18:14787040:A", "Test", "Hsa/jun2011")
-  GENOTYPE = GenomicMutation.setup(Rbbt.data.genotype.list, "Test", "Hsa/jun2011")
-
-  def test_genes
-    assert GENOTYPE.genes.flatten.to("Associated Gene Name").include? "PSTK"
-  end
-
-  def test_consolidate
-    assert GENOTYPE.genes.consolidate.to("Associated Gene Name").include? "PSTK"
-  end
 
   def test_mutated_isoforms
     assert MUTATION.mutated_isoforms.length > 1
@@ -32,7 +23,6 @@ class TestGenomicMutation < Test::Unit::TestCase
     assert MUTATION.over_gene? Gene.setup("PSTK", "Associated Gene Name", "Hsa/jun2011").ensembl
     assert(!(SPLICING.over_gene? Gene.setup("PSTK", "Associated Gene Name", "Hsa/jun2011").ensembl))
   end
-
 end
 
 

data/test/rbbt/test_entity.rb

@@ -0,0 +1,101 @@
+require File.expand_path(File.dirname(__FILE__) + '/../test_helper')
+require 'rbbt/entity'
+require 'rbbt/util/tmpfile'
+require 'test/unit'
+
+module ReversableString
+  extend Entity
+  
+  property :reverse_text_ary => :array do
+    $count += 1
+    self.collect{|s| s.reverse}
+  end
+ 
+  property :reverse_text_single => :single do
+    $count += 1
+    self.reverse
+  end
+
+  property :reverse_text_ary_p => :array do
+    $count += 1
+    self.collect{|s| s.reverse}
+  end
+ 
+  property :reverse_text_single_p => :single do
+    $count += 1
+    self.reverse
+  end
+
+  property :reverse_text_ary_p_array => :array do
+    $count += 1
+    self.collect{|s| s.reverse}
+  end
+ 
+  persist :reverse_text_ary_p
+  persist :reverse_text_ary_p
+  persist :reverse_text_ary_p
+  persist :reverse_text_single_p
+
+  persist :reverse_text_ary_p_array, :array, :dir => TmpFile.tmp_file
+end
+class TestEntity < Test::Unit::TestCase
+
+  def test_property_ary
+    a = ["String1", "String2"]
+    a.extend ReversableString
+
+    $count = 0
+
+    assert_equal "2gnirtS", a.reverse_text_ary.last
+    assert_equal 1, $count
+    assert_equal "2gnirtS", a[1].reverse_text_ary
+    assert_equal 2, $count
+  end
+
+  def test_property_single
+    a = ["String1", "String2"]
+    a.extend ReversableString
+
+    $count = 0
+
+    assert_equal "2gnirtS", a.reverse_text_single.last
+    assert_equal 2, $count
+    assert_equal "2gnirtS", a[1].reverse_text_single
+    assert_equal 3, $count
+  end
+
+  def test_property_ary_p
+    a = ["String1", "String2"]
+    a.extend ReversableString
+
+    $count = 0
+
+    assert_equal "2gnirtS", a.reverse_text_ary_p.last
+    assert_equal "2gnirtS", a[1].reverse_text_ary_p
+    assert_equal 1, $count
+  end
+
+  def test_property_single_p
+    a = ["String1", "String2"]
+    a.extend ReversableString
+
+    $count = 0
+
+    assert_equal "2gnirtS", a.reverse_text_single_p.last
+    assert_equal 2, $count
+    assert_equal "2gnirtS", a[1].reverse_text_single_p
+    assert_equal 2, $count
+  end
+
+  def test_property_ary_p_array
+    a = ["String1", "String2"]
+    a.extend ReversableString
+
+    $count = 0
+
+    assert_equal "2gnirtS", a.reverse_text_ary_p_array.last
+    assert_equal 1, $count
+    assert_equal "2gnirtS", a.reverse_text_ary_p_array.last
+    assert_equal 1, $count
+  end
+end

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: rbbt-entities
 version: !ruby/object:Gem::Version 
-  hash: 23
+  hash: 19
   prerelease: 
   segments: 
   - 1
+  - 1
   - 0
-  - 0
-  version: 1.0.0
+  version: 1.1.0
 platform: ruby
 authors: 
 - Miguel Vazquez
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-11-17 00:00:00 +01:00
+date: 2012-01-13 00:00:00 +01:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -79,6 +79,7 @@ files:
 - lib/rbbt/entity/mutated_isoform.rb
 - lib/rbbt/entity/pmid.rb
 - lib/rbbt/entity/protein.rb
+- lib/rbbt/entity/transcript.rb
 - test/test_helper.rb
 - test/rbbt/entity/test_gene.rb
 - test/rbbt/entity/test_genomic_mutation.rb