rbbt-sources 1.2.0 → 2.0.0

data/test/rbbt/sources/test_organism.rb

@@ -1,17 +1,22 @@
 require File.expand_path(File.dirname(__FILE__) + '/../../test_helper')
 require 'rbbt/sources/organism'
 require 'test/unit'
+require 'rbbt/sources/ensembl_ftp'
+
+class TestOrganism < Test::Unit::TestCase
+
+  def test_known_ids
+    assert Organism.known_ids("Hsa").include?("Associated Gene Name")
+  end
 
-class TestEntrez < Test::Unit::TestCase
   def test_location
     assert_equal "share/organisms/Sce/identifiers", Organism.identifiers('Sce')
   end
 
-
   def test_identifiers
     assert Organism.identifiers('Hsa').tsv(:key_field => "Entrez Gene ID", :persist => true)['1020']["Associated Gene Name"].include?('CDK5')
     assert Organism.identifiers('Sce').tsv(:persist => true)['S000006120']["Ensembl Gene ID"].include?('YPL199C')
-    assert Organism::Sce.identifiers.tsv(:persist => true)['S000006120']["Ensembl Gene ID"].include?('YPL199C')
+    assert Organism.identifiers("Sce").tsv(:persist => true)['S000006120']["Ensembl Gene ID"].include?('YPL199C')
   end
 
   def test_lexicon
@@ -21,8 +26,8 @@ class TestEntrez < Test::Unit::TestCase
   def test_guess_id
     ensembl = %w(YOL044W YDR289C YAL034C YGR246C ARS519 tH(GUG)E2 YDR218C YLR002C YGL224C)
     gene_name = %w(SNR64 MIP1 MRPS18 TFB2 JEN1 IVY1 TRS33 GAS3)
-    assert_equal "Associated Gene Name", Organism::Sce.guess_id(gene_name).first
-    assert_equal "Ensembl Gene ID", Organism::Sce.guess_id(ensembl).first
+    assert_equal "Associated Gene Name", Organism.guess_id("Sce", gene_name).first
+    assert_equal "Ensembl Gene ID", Organism.guess_id("Sce", ensembl).first
   end
 
   def test_organisms
@@ -36,12 +41,26 @@ class TestEntrez < Test::Unit::TestCase
     tsv.fields = []
     tsv.namespace = "Hsa"
     
-    Organism::Hsa.attach_translations tsv, "Associated Gene Name"
-    Organism::Hsa.attach_translations tsv, "Ensembl Gene ID"
+    Organism.attach_translations "Hsa", tsv, "Associated Gene Name"
+    Organism.attach_translations "Hsa", tsv, "Ensembl Gene ID"
 
     assert_equal "CDK5", tsv["1020"]["Associated Gene Name"]
   end
 
+  def test_entrez_taxids
+    assert_equal "Hsa", Organism.entrez_taxid_organism('9606')
+  end
+
+  def test_lift_over
+    mutation_19 = "19:21131664:T"
+    mutation_18 = "19:20923504:T"
+    source_build = "Hsa/jun2011"
+    target_build = "Hsa/may2009"
+
+    assert_equal mutation_18, Organism.liftOver([mutation_19], source_build, target_build).first
+    assert_equal mutation_19, Organism.liftOver([mutation_18], target_build, source_build).first
+  end
+
   #def test_genes_at_chromosome
   #  pos = [12, 117799500]
   #  assert_equal "ENSG00000089250", Organism::Hsa.genes_at_chromosome_positions(pos.first, pos.last)

data/test/rbbt/sources/test_pubmed.rb

@@ -30,6 +30,11 @@ class TestPubMed < Test::Unit::TestCase
     assert(PubMed.query('chagoyen[All Fields] AND ("loattrfull text"[sb] AND hasabstract[text])').include? '16438716')
   end
 
+  def test_year
+    pmid = '16438716'
+    assert_equal "2006", PubMed.get_article(pmid).year
+  end
+
   def test_bibentry
     assert("vazquez2008sent", PubMed::Article.make_bibentry('vazquez', 2008, "SENT: Semantic features in text"))
     assert("vazquez2008aes", PubMed::Article.make_bibentry('vazquez', 2008, "An Example System"))

metadata

@@ -1,115 +1,119 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: rbbt-sources
-version: !ruby/object:Gem::Version 
-  hash: 31
+version: !ruby/object:Gem::Version
+  version: 2.0.0
   prerelease: 
-  segments: 
-  - 1
-  - 2
-  - 0
-  version: 1.2.0
 platform: ruby
-authors: 
+authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2012-01-13 00:00:00 +01:00
-default_executable: 
-dependencies: 
-- !ruby/object:Gem::Dependency 
+date: 2012-12-21 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
   name: rbbt-util
-  prerelease: false
-  requirement: &id001 !ruby/object:Gem::Requirement 
+  requirement: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 63
-        segments: 
-        - 4
-        - 0
-        - 0
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
         version: 4.0.0
   type: :runtime
-  version_requirements: *id001
-- !ruby/object:Gem::Dependency 
-  name: rbbt-text
   prerelease: false
-  requirement: &id002 !ruby/object:Gem::Requirement 
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 4.0.0
+- !ruby/object:Gem::Dependency
+  name: rbbt-text
+  requirement: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :runtime
-  version_requirements: *id002
-- !ruby/object:Gem::Dependency 
-  name: mechanize
   prerelease: false
-  requirement: &id003 !ruby/object:Gem::Requirement 
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
-  type: :runtime
-  version_requirements: *id003
-- !ruby/object:Gem::Dependency 
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
   name: libxml-ruby
-  prerelease: false
-  requirement: &id004 !ruby/object:Gem::Requirement 
+  requirement: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :runtime
-  version_requirements: *id004
-- !ruby/object:Gem::Dependency 
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
   name: bio
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
   prerelease: false
-  requirement: &id005 !ruby/object:Gem::Requirement 
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: mechanize
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :runtime
-  version_requirements: *id005
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 description: Data sources like PubMed, Entrez Gene, or Gene Ontology
 email: miguel.vazquez@fdi.ucm.es
 executables: []
-
 extensions: []
-
 extra_rdoc_files: []
-
-files: 
+files:
 - etc/biomart/missing_in_archive
 - lib/rbbt/sources/COSMIC.rb
 - lib/rbbt/sources/COSTART.rb
 - lib/rbbt/sources/CTCAE.rb
+- lib/rbbt/sources/HPRD.rb
 - lib/rbbt/sources/InterPro.rb
 - lib/rbbt/sources/NCI.rb
+- lib/rbbt/sources/PSI_MI.rb
+- lib/rbbt/sources/STITCH.rb
 - lib/rbbt/sources/barcode.rb
 - lib/rbbt/sources/bibtex.rb
 - lib/rbbt/sources/biomart.rb
 - lib/rbbt/sources/cath.rb
+- lib/rbbt/sources/dbSNP.rb
+- lib/rbbt/sources/ensembl_ftp.rb
 - lib/rbbt/sources/entrez.rb
+- lib/rbbt/sources/genomes1000.rb
 - lib/rbbt/sources/go.rb
 - lib/rbbt/sources/gscholar.rb
 - lib/rbbt/sources/jochem.rb
@@ -117,10 +121,12 @@ files:
 - lib/rbbt/sources/pfam.rb
 - lib/rbbt/sources/polysearch.rb
 - lib/rbbt/sources/pubmed.rb
+- lib/rbbt/sources/reactome.rb
 - lib/rbbt/sources/tfacts.rb
 - lib/rbbt/sources/uniprot.rb
 - lib/rbbt/sources/wgEncodeBroadHmm.rb
-- share/install/InterPro/Rakefile
+- share/Ensembl/release_dates
+- share/install/Genomes1000/Rakefile
 - share/install/JoChem/Rakefile
 - share/install/NCI/Rakefile
 - share/install/Organism/Hsa/Rakefile
@@ -128,6 +134,7 @@ files:
 - share/install/Organism/Rno/Rakefile
 - share/install/Organism/Sce/Rakefile
 - share/install/Organism/organism_helpers.rb
+- share/install/STITCH/Rakefile
 - share/install/lib/helpers.rb
 - test/test_helper.rb
 - test/rbbt/sources/test_entrez.rb
@@ -135,41 +142,31 @@ files:
 - test/rbbt/sources/test_go.rb
 - test/rbbt/sources/test_biomart.rb
 - test/rbbt/sources/test_organism.rb
-has_rdoc: true
 homepage: http://github.com/mikisvaz/rbbt-sources
 licenses: []
-
 post_install_message: 
 rdoc_options: []
-
-require_paths: 
+require_paths:
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement 
+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 
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
-      - 0
-      version: "0"
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
 requirements: []
-
 rubyforge_project: 
-rubygems_version: 1.6.2
+rubygems_version: 1.8.24
 signing_key: 
 specification_version: 3
 summary: Data sources for the Ruby Bioinformatics Toolkit (rbbt)
-test_files: 
+test_files:
 - test/test_helper.rb
 - test/rbbt/sources/test_entrez.rb
 - test/rbbt/sources/test_pubmed.rb

data/share/install/InterPro/Rakefile

@@ -1,29 +0,0 @@
-$LOAD_PATH.unshift(File.join(File.dirname(__FILE__),'..', '..', '..', '..', 'lib'))
-require 'rbbt/sources/biomart'
-require 'rbbt/sources/entrez'
-
-$interpro_db = 'entry'
-
-$interpro_id = ['InterPro Entry Accession','entry_id']
-
-$interpro_pos = [
-  ["UniProt/SwissProt Accession", "protein_ac"],
-  ["Match Start Position", "pos_from"],
-  ["Match Stop Position ", "pos_to"]
-]
-
-file 'interpro_positions' do |t|
-  Open.write(t.name, InterPro.tsv($interpro_db, $interpro_id, $interpro_pos, [], nil, :type => :double, :nocache => true).to_s)
-end
-
-file 'interpro_names' do |t|
-  Open.write(t.name, "#: :type=:list\n#InterPro Entry Accession\tName\n" +  Open.read("ftp://ftp.ebi.ac.uk/pub/databases/interpro/names.dat"))
-end
-
-
-file 'interpro_short_names' do |t|
-  Open.write(t.name,  "#: :type=:list\n#InterPro Entry Accession\tShort Name\n" +  Open.read("ftp://ftp.ebi.ac.uk/pub/databases/interpro/short_names.dat"))
-end
-
-
-