ruby-ensembl-api 1.0 → 1.0.1

data/lib/ensembl.rb

@@ -6,6 +6,8 @@
 #                           
 # License::     The Ruby License
 #
+# @author Jan Aerts
+# @author Francesco Strozzi
 
 module Ensembl
   ENSEMBL_RELEASE = 60

data/lib/ensembl/core/activerecord.rb

@@ -1070,7 +1070,8 @@ module Ensembl
         xrefs.each do |xref|
           answer.push(Ensembl::Core::Gene.find_by_display_xref_id(xref.xref_id))
         end
-      
+        
+        answer.reject!{|a| a.nil?}
       	return answer
       end
       

data/lib/ensembl/core/slice.rb

@@ -593,12 +593,12 @@ SQL
       
       # Method to retrieve Variation features from Ensembl::Core::Slice objects
       # @example
-      # slice = Slice.fetch_by_region('chromosome',1,50000,51000)
-      # variations = slice.get_variation_features
-      # variations.each do |vf|
-      #  puts vf.variation_name, vf.allele_string
-      #  puts vf.variation.ancestral_allele
-      # end
+      #   slice = Slice.fetch_by_region('chromosome',1,50000,51000)
+      #   variations = slice.get_variation_features
+      #   variations.each do |vf|
+      #    puts vf.variation_name, vf.allele_string
+      #    puts vf.variation.ancestral_allele
+      #   end
       def get_variation_features
         variation_connection()
         Ensembl::Variation::VariationFeature.find(:all,:conditions => ["seq_region_id = ? AND seq_region_start >= ? AND seq_region_end <= ?",self.seq_region.seq_region_id,self.start,self.stop])

data/lib/ensembl/db_connection.rb

@@ -20,9 +20,7 @@ module Ensembl
   EG_PORT = 4157
 
 
-  # = DESCRIPTION
   # Generic class to perform dynamic connections to the Ensembl database and retrieve database names
-  #
   class DummyDBConnection < ActiveRecord::Base
     self.abstract_class = true
     def self.connect(args)
@@ -38,11 +36,9 @@ module Ensembl
   end
 
   module DBRegistry 
-    # = DESCRIPTION
     # The Ensembl::Registry::Base is a super class providing general methods 
     # to get database and connection info.
     class Base < ActiveRecord::Base
-        
       self.abstract_class = true
       self.pluralize_table_names = false
       def self.get_info
@@ -55,7 +51,7 @@ module Ensembl
           return host,user,password,db_name,port,species,release.to_i
         end
       end
-      # = DESCRIPTION
+      
       # Method to retrieve the name of a database, using species, release and connection parameters
       # passed by the user.    
       def self.get_name_from_db(db_type,species,release,args)
@@ -121,30 +117,25 @@ module Ensembl
   
   
   module Core
-    # = DESCRIPTION
     # The Ensembl::Core::DBConnection is the actual connection established
     # with the Ensembl server.
     class DBConnection < Ensembl::DBRegistry::Base
       self.abstract_class = true
       self.pluralize_table_names = false
-      # = DESCRIPTION
       # The Ensembl::Core::DBConnection#connect method makes the connection
       # to the Ensembl core database for a given species. By default, it connects
       # to release 50 for that species. You _could_ use a lower number, but
       # some parts of the API might not work, or worse: give the wrong results.
       #
-      # = USAGE
+      # @example
       #  # Connect to release 50 of human
       #  Ensembl::Core::DBConnection.connect('homo_sapiens')
       #
       #  # Connect to release 42 of chicken
       #  Ensembl::Core::DBConnection.connect('gallus_gallus')
       #
-      # ---
-      # *Arguments*:
-      # * species:: species to connect to. Arguments should be in snake_case
-      # * ensembl_release:: the release of the database to connect to
-      #  (default = 50)      
+      # @param [String] species Species to connect to. Must be in snake_case
+      # @param [Integer] ensembl_release. Release to connect to (default = 60)
       def self.connect(species, release = Ensembl::ENSEMBL_RELEASE, args = {})
         self.generic_connect('core',species, release,args)
       end
@@ -160,30 +151,25 @@ module Ensembl
   end # Core
 
   module Variation
-    # = DESCRIPTION
     # The Ensembl::Variation::DBConnection is the actual connection established
     # with the Ensembl server.
     class DBConnection < Ensembl::DBRegistry::Base
       self.abstract_class = true
       self.pluralize_table_names = false
-      # = DESCRIPTION
       # The Ensembl::Variation::DBConnection#connect method makes the connection
       # to the Ensembl variation database for a given species. By default, it connects
       # to release 50 for that species. You _could_ use a lower number, but
       # some parts of the API might not work, or worse: give the wrong results.
       #
-      # = USAGE
+      # @example
       #  # Connect to release 50 of human
       #  Ensembl::Variation::DBConnection.connect('homo_sapiens')
       #
       #  # Connect to release 42 of chicken
       #  Ensembl::Variation::DBConnection.connect('gallus_gallus')
       #
-      # ---
-      # *Arguments*:
-      # * species:: species to connect to. Arguments should be in snake_case
-      # * ensembl_release:: the release of the database to connect to
-      #  (default = 50)
+      # @param [String] species Species to connect to. Must be in snake_case
+      # @param [Integer] ensembl_release. Release to connect to (default = 60)
       def self.connect(species, release = Ensembl::ENSEMBL_RELEASE, args = {})
         self.generic_connect('variation',species, release, args)
       end

data/lib/ensembl/variation/activerecord.rb

@@ -19,7 +19,7 @@ module Ensembl
     # See the general documentation of the Ensembl module for
     # more information on what this means and what methods are available.
     #
-    # = USAGE
+    # @example
     #  allele = Allele.find(1)
     #  puts allele.to_yaml
     class Allele < DBConnection
@@ -30,7 +30,6 @@ module Ensembl
       belongs_to :subsnp_handle
     end
 
-    # = DESCRIPTION
     # The AlleleGroup class represents a grouping of alleles that have tight 
     # linkage and are usually present together. This is commonly known as a 
     # Haplotype or Haplotype Block. 
@@ -39,7 +38,7 @@ module Ensembl
     # See the general documentation of the Ensembl module for
     # more information on what this means and what methods are available.
     #
-    # = USAGE
+    # @example
     #  allele_group = AlleleGroup.find(1)
     #  puts allele_group.to_yaml
     class AlleleGroup < DBConnection
@@ -50,7 +49,6 @@ module Ensembl
       belongs_to :allele_group_allele
     end
     
-    # = DESCRIPTION
     # The AlleleGroupAllele class represents a connection class between Allele and AlleleGroup. 
     # Should not be used directly.
     #
@@ -62,7 +60,6 @@ module Ensembl
       belongs_to :allele_group
     end
     
-    # = DESCRIPTION
     # Store information on attributes types
     #
     # This class uses ActiveRecord to access data in the Ensembl database.
@@ -72,9 +69,6 @@ module Ensembl
       set_primary_key "attrib_type_id"
     end 
     
-    
-    # = DESCRIPTION
-    # 
     # This class uses ActiveRecord to access data in the Ensembl database.
     # See the general documentation of the Ensembl module for
     # more information on what this means and what methods are available.    
@@ -82,8 +76,6 @@ module Ensembl
       
     end
 
-    # = DESCRIPTION
-    # 
     # This class uses ActiveRecord to access data in the Ensembl database.
     # See the general documentation of the Ensembl module for
     # more information on what this means and what methods are available.    
@@ -92,8 +84,6 @@ module Ensembl
       has_many :failed_variations
     end
     
-    # = DESCRIPTION
-    # 
     # This class uses ActiveRecord to access data in the Ensembl database.
     # See the general documentation of the Ensembl module for
     # more information on what this means and what methods are available.    
@@ -103,8 +93,6 @@ module Ensembl
       belongs_to :variation
     end    
     
-    # = DESCRIPTION
-    # 
     # This class uses ActiveRecord to access data in the Ensembl database.
     # See the general documentation of the Ensembl module for
     # more information on what this means and what methods are available.    
@@ -125,9 +113,6 @@ module Ensembl
       has_many :variation_annotations
     end
     
-    
-    
-    # = DESCRIPTION
     # The Sample class gives information about the biological samples stored in the database. 
     #
     # This class uses ActiveRecord to access data in the Ensembl database.
@@ -155,7 +140,6 @@ module Ensembl
       belongs_to :population, :foreign_key => "population_sample_id"
     end
     
-    # = DESCRIPTION
     # The Individual class gives information on the single individuals used 
     # to retrieve one or more biological samples.
     #
@@ -207,7 +191,6 @@ module Ensembl
       
     end
     
-    # = DESCRIPTION
     # The PopulationGenotype class gives information about alleles and allele 
     # frequencies for a SNP observed within a population or a group of samples. 
     #
@@ -222,7 +205,6 @@ module Ensembl
       has_many :compressed_genotype_single_bps, :foreign_key => "sample_id"
     end
     
-    # = DESCRIPTION
     # The SampleSynonym class represents information about alternative names 
     # for sample entries. 
     #
@@ -236,7 +218,6 @@ module Ensembl
       belongs_to :population
     end
     
-    # = DESCRIPTION
     # The Source class gives information on the different databases and SNP 
     # panels used to retrieve the data
     #
@@ -288,7 +269,6 @@ module Ensembl
       has_many :variation_synonyms,:foreign_key => "subsnp_id"
     end
     
-    # = DESCRIPTION
     # The VariationSynonym class gives information on alterative names used 
     # for Variation entries. 
     #
@@ -302,7 +282,6 @@ module Ensembl
       belongs_to :subsnp_handle
     end
         
-    # = DESCRIPTION
     # The VariationGroup class represents a group of variations (SNPs) that are 
     # linked and present toghether. 
     #
@@ -318,7 +297,6 @@ module Ensembl
       has_one :allele_group
     end
     
-    # = DESCRIPTION
     # The VariationGroupVariation class is a connection class. 
     # Should not be used directly.
     #
@@ -330,7 +308,6 @@ module Ensembl
       belongs_to :variation_group
     end
     
-    # = DESCRIPTION
     # The VariationGroupFeature class gives information on the genomic position 
     # of each VariationGroup.
     #
@@ -350,7 +327,6 @@ module Ensembl
     end
     
     
-    # = DESCRIPTION
     # The FlankingSequence class gives information about the genomic coordinates 
     # of the flanking sequences, for a single VariationFeature. 
     #
@@ -361,7 +337,6 @@ module Ensembl
       belongs_to :variation
     end
     
-    # = DESCRIPTION
     # The TaggedVariationFeature class is a connection class. 
     # Should not be used directly.
     #

metadata

@@ -1,7 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: ruby-ensembl-api
 version: !ruby/object:Gem::Version 
-  version: "1.0"
+  hash: 21
+  prerelease: false
+  segments: 
+  - 1
+  - 0
+  - 1
+  version: 1.0.1
 platform: ruby
 authors: 
 - Jan Aerts
@@ -10,29 +16,37 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-12-15 00:00:00 +01:00
+date: 2010-12-16 00:00:00 +01:00
 default_executable: ensembl
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: bio
-  type: :runtime
-  version_requirement: 
-  version_requirements: !ruby/object:Gem::Requirement 
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
+        hash: 1
+        segments: 
+        - 1
         version: "1"
-    version: 
+  type: :runtime
+  version_requirements: *id001
 - !ruby/object:Gem::Dependency 
   name: activerecord
-  type: :runtime
-  version_requirement: 
-  version_requirements: !ruby/object:Gem::Requirement 
+  prerelease: false
+  requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
         version: "0"
-    version: 
+  type: :runtime
+  version_requirements: *id002
 description: ruby-ensembl-api provides a ruby API to the Ensembl databases (http://www.ensembl.org)
 email: 
 - jan.aerts@gmail.com
@@ -71,7 +85,7 @@ files:
 - test/unit/test_connection.rb
 - test/unit/test_releases.rb
 - TUTORIAL.rdoc
-has_rdoc: true
+has_rdoc: yard
 homepage: http://github.com/jandot/ruby-ensembl-api
 licenses: []
 
@@ -81,21 +95,27 @@ 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"
-  version: 
 required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
       version: "0"
-  version: 
 requirements: []
 
 rubyforge_project: 
-rubygems_version: 1.3.5
+rubygems_version: 1.3.7
 signing_key: 
 specification_version: 3
 summary: API to Ensembl databases