rbbt-sources 0.2.2 → 0.3.1

data/share/install/lib/helpers.rb

@@ -7,10 +7,10 @@ def tsv_file(url, native, extra, options = {})
 
   case
   when Array === native
-    options = Misc.add_defaults options, :native => native.last 
+    options = Misc.add_defaults options, :key => native.last 
     key_field = native.first
   when (String === native or Integer === native)
-    options = Misc.add_defaults options, :native => native
+    options = Misc.add_defaults options, :key => native
     key_field = nil
   else
     key_field = nil
@@ -18,10 +18,10 @@ def tsv_file(url, native, extra, options = {})
 
   case
   when (Array === extra and Array === extra.first)
-    options = Misc.add_defaults options, :extra => extra.collect{|e| e.last}
+    options = Misc.add_defaults options, :fields => extra.collect{|e| e.last}
     fields = extra.collect{|e| e.first}
   when (Array === extra and not Array === extra.first)
-    options = Misc.add_defaults options, :extra => extra
+    options = Misc.add_defaults options, :fields => extra
     fields = (1..extra.length).to_a.collect{|i| "Field#{i}"}
   else
     fields = nil
@@ -29,7 +29,7 @@ def tsv_file(url, native, extra, options = {})
 
   tsv = TSV.new(Open.open(url), options)
   tsv.key_field ||= key_field
-  tsv.fields ||= fields
+  tsv.fields    ||= fields
   tsv
 end
 

data/test/rbbt/sources/test_biomart.rb

@@ -4,17 +4,18 @@ require 'test/unit'
 
 class TestBioMart < Test::Unit::TestCase
 
-  def _test_get
+  def test_get
     assert_raise BioMart::QueryError do 
       BioMart.get('scerevisiae_gene_ensembl','entrezgene', ['protein_id'],['with_unknownattr'])
     end
 
-    data = BioMart.get('scerevisiae_gene_ensembl','entrezgene', ['protein_id'],[], nil, :nocache => false, :wget_options => { :quiet => false})
-    assert(data['852236']['protein_id'].include? 'CAA84864')
+    data = BioMart.get('scerevisiae_gene_ensembl','entrezgene', ['protein_id'],[], nil, :nocache => false, :merge => true, :wget_options => {:quiet => false})
+    tsv = TSV.new data, :double, :merge => true
+    assert(tsv['852236'][0].include? 'CAA84864')
 
     data = BioMart.get('scerevisiae_gene_ensembl','entrezgene', ['external_gene_id'],[], data, :nocache => false, :wget_options => { :quiet => false} )
-    assert(data['852236']['protein_id'].include? 'CAA84864')
-    assert(data['852236']['external_gene_id'].include? 'YBL044W')
+    tsv = TSV.new data, :double, :merge => true
+    assert(tsv['852236'][1].include? 'YBL044W')
   end
 
   def test_query
@@ -23,7 +24,7 @@ class TestBioMart < Test::Unit::TestCase
     assert(data['852236']['external_gene_id'].include? 'YBL044W')
   end
 
-  def _test_tsv
+  def test_tsv
     data = BioMart.tsv('scerevisiae_gene_ensembl',['Entrez Gene', 'entrezgene'], [['Protein ID', 'protein_id'],['RefSeq Peptide','refseq_peptide']], [], nil, :nocache => false, :wget_options => { :quiet => false})
 
     assert(data['852236']['Protein ID'].include? 'CAA84864')

data/test/rbbt/sources/test_entrez.rb

@@ -3,12 +3,12 @@ require 'rbbt/sources/entrez'
 require 'test/unit'
 
 class TestEntrez < Test::Unit::TestCase
-  $yeast_tax = [559292,4932]
+  $yeast_tax = 559292
 
   def test_entrez2native
     tax    = $yeast_tax
     fix    = proc{|line| line.sub(/SGD:S0/,'S0') }
-    select = proc{|line| line.match(/\tS0/)}
+    select = proc{|line| line.match(/SGD:S0/)}
     lexicon = Entrez.entrez2native(tax, :fix => fix, :select => select)
 
     assert(lexicon['855611'].include? 'S000005056') 
@@ -40,7 +40,7 @@ class TestEntrez < Test::Unit::TestCase
 
   def test_similarity
     assert(Entrez.gene_text_similarity(9129, "PRP3 pre-mRNA processing factor 3 homolog (S. cerevisiae)") > 0)
-    assert_equal(0, Entrez.gene_text_similarity("NON EXISTEN GENEID", "PRP3 pre-mRNA processing factor 3 homolog (S. cerevisiae)"))
+    assert_equal(0, Entrez.gene_text_similarity("NON EXISTENT GENEID", "PRP3 pre-mRNA processing factor 3 homolog (S. cerevisiae)"))
   end
 
 end

data/test/rbbt/sources/test_organism.rb

@@ -1,12 +1,13 @@
 require File.expand_path(File.dirname(__FILE__) + '/../../test_helper')
 require 'rbbt/sources/organism'
+require 'rbbt/sources/organism/sequence'
 require 'test/unit'
 
 class TestEntrez < Test::Unit::TestCase
   def test_identifiers
-    assert TSV.new(Organism.identifiers('Sce'))['S000006120']["Ensembl Gene ID"].include?('YPL199C')
-    assert TSV.new(Organism::Sce.identifiers)['S000006120']["Ensembl Gene ID"].include?('YPL199C')
-    assert TSV.new(Organism.identifiers('Hsa'))['1020']["Associated Gene Name"].include?('CDK5')
+    assert Organism.identifiers('Sce').tsv['S000006120']["Ensembl Gene ID"].include?('YPL199C')
+    assert Organism::Sce.identifiers.tsv['S000006120']["Ensembl Gene ID"].include?('YPL199C')
+    assert Organism.identifiers('Hsa').tsv(:key => "Entrez Gene ID")['1020']["Associated Gene Name"].include?('CDK5')
   end
 
   def test_lexicon
@@ -24,6 +25,34 @@ class TestEntrez < Test::Unit::TestCase
     assert Organism.organisms.include? "Hsa"
     assert_equal "Hsa", Organism.organism("Homo sapiens")
   end
+
+  def test_attach_translations
+    tsv = TSV.new({"1020" => []}, :list)
+    tsv.key_field = "Entrez Gene ID"
+    tsv.fields = []
+    tsv.namespace = "Hsa"
+    
+    Organism::Hsa.attach_translations tsv, "Associated Gene Name"
+    Organism::Hsa.attach_translations tsv, "Ensembl Gene ID"
+
+    assert_equal "CDK5", tsv["1020"]["Associated Gene Name"]
+  end
+
+  def test_genes_at_chromosome
+    pos = [12, 117799500]
+    assert_equal "ENSG00000089250", Organism::Hsa.genes_at_chromosome_positions(pos.first, pos.last)
+  end
+
+  def test_genes_at_chromosome_array
+    pos = [12, [117799500, 106903900]]
+    assert_equal ["ENSG00000089250", "ENSG00000013503"], Organism::Hsa.genes_at_chromosome_positions(pos.first, pos.last)
+  end
+ 
+  def test_genes_at_genomic_positions
+    pos = [[12, 117799500], [12, 106903900], [1, 115259500]]
+    assert_equal ["ENSG00000089250", "ENSG00000013503", "ENSG00000213281"], Organism::Hsa.genes_at_genomic_positions(pos)
+  end
+
 end
 
 

data/test/rbbt/sources/test_pubmed.rb

@@ -21,7 +21,7 @@ class TestPubMed < Test::Unit::TestCase
     assert(PubMed.get_article(pmids)[pmid].title == "Discovering semantic features in the literature: a foundation for building functional associations.")
   end
  
-  def _test_full_text
+  def test_full_text
     pmid = '16438716'
     assert(PubMed.get_article(pmid).full_text =~ /Discovering/)
   end

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: rbbt-sources
 version: !ruby/object:Gem::Version 
-  hash: 19
+  hash: 17
   prerelease: 
   segments: 
   - 0
-  - 2
-  - 2
-  version: 0.2.2
+  - 3
+  - 1
+  version: 0.3.1
 platform: ruby
 authors: 
 - Miguel Vazquez
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-01-30 00:00:00 +01:00
+date: 2011-03-19 00:00:00 +01:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -85,17 +85,18 @@ extra_rdoc_files: []
 files: 
 - lib/rbbt/sources/COSTART.rb
 - lib/rbbt/sources/CTCAE.rb
-- lib/rbbt/sources/Reactome.rb
 - lib/rbbt/sources/bibtex.rb
 - lib/rbbt/sources/biomart.rb
 - lib/rbbt/sources/entrez.rb
 - lib/rbbt/sources/go.rb
 - lib/rbbt/sources/gscholar.rb
 - lib/rbbt/sources/organism.rb
+- lib/rbbt/sources/organism/sequence.rb
 - lib/rbbt/sources/polysearch.rb
 - lib/rbbt/sources/pubmed.rb
 - share/install/Organism/Hsa/Rakefile
 - share/install/Organism/Sce/Rakefile
+- share/install/Organism/organism_helpers.rb
 - share/install/lib/helpers.rb
 - test/rbbt/sources/test_biomart.rb
 - test/rbbt/sources/test_entrez.rb

data/lib/rbbt/sources/Reactome.rb

@@ -1,16 +0,0 @@
-require 'rbbt-util'
-
-module Reactome
-
-  Rbbt.claim "Reactome", 
-    Proc.new do
-      headers = ["Uniprot ID#1", "Ensembl Gene ID#2","Entrez Gene ID#1", "Uniprot ID#2", "Ensembl Gene ID#2", "Entrez Gene ID#2" , "Type", "Reaction", "PMID"]
-
-      tsv = TSV.new(Open.open("http://www.reactome.org/download/current/homo_sapiens.interactions.txt.gz"), :fix => Proc.new {|l| l.gsub(/[\w ]+:/, "")})
-      tsv.key_field = headers.shift
-      tsv.fields    = headers
-
-      tsv.to_s
-    end, 'Reactome'
-  ]
-end