bio-ensembl-rest 0.1.0

data/lib/bio-ensembl-rest/features.rb

@@ -0,0 +1,46 @@
+module EnsemblRest
+  module Features
+
+    ##
+    # Uses the given identifier as a way of indicating the Slice of features required
+    def self.feature_id(id, features, opts = {})
+      opts = EnsemblRest.parse_options opts
+
+      # features is a required parameter, but we need to encode it into the url
+      encoded_query = ""
+      features.each {|f| encoded_query << "feature=#{f};"}
+
+      path = (EnsemblRest.build_path "/feature/id/#{id}", opts) + encoded_query
+
+      if opts['content-type'] == 'ruby'
+        plain_opts = opts.clone
+        plain_opts['content-type'] = 'application/json'
+        return JSON.parse feature_id id, features, plain_opts
+      end
+
+      return EnsemblRest.fetch_data path, opts, 'features'   
+    end
+
+
+    ##
+    # Retrieves multiple types of features for a given region
+    def self.feature_region(species, region, features, opts = {})
+      opts = EnsemblRest.parse_options opts
+
+      # features is a required parameter, but we need to encode it into the url
+      encoded_query = ""
+      features.each {|f| encoded_query << "feature=#{f};"}
+
+      path = (EnsemblRest.build_path "/feature/region/#{species}/#{region}", opts) + encoded_query
+
+      if opts['content-type'] == 'ruby'
+        plain_opts = opts.clone
+        plain_opts['content-type'] = 'application/json'
+        return JSON.parse feature_region species, region, features, plain_opts
+      end
+
+      return EnsemblRest.fetch_data path, opts, 'features'   
+    end
+
+  end
+end

data/lib/bio-ensembl-rest/information.rb

@@ -0,0 +1,133 @@
+module EnsemblRest
+  module Information
+
+    ##
+    # Returns information about the current available assemblies in this given species
+    def self.assembly_info(species, opts = {})
+      opts = EnsemblRest.parse_options opts
+      path = EnsemblRest.build_path "/assembly/info/#{species}", opts
+
+      if opts['content-type'] == 'ruby'
+        plain_opts = opts.clone
+        plain_opts['content-type'] = 'application/json'
+        return JSON.parse assembly_info species, plain_opts
+      end
+
+      return EnsemblRest.fetch_data path, opts, 'information'  
+    end
+
+
+    ##
+    # Returns information about the given toplevel sequence region given to this endpoint
+    def self.assembly_info_region(species, region, opts = {})
+      opts = EnsemblRest.parse_options opts
+      path = EnsemblRest.build_path "/assembly/info/#{species}/#{region}", opts
+
+      if opts['content-type'] == 'ruby'
+        plain_opts = opts.clone
+        plain_opts['content-type'] = 'application/json'
+        return JSON.parse assembly_info_region species, plain_opts
+      end
+
+      return EnsemblRest.fetch_data path, opts, 'information'        
+    end
+
+
+    ##
+    # Lists all available comparative genomics databases and their data release
+    def self.info_comparas(opts = {})
+      opts = EnsemblRest.parse_options opts
+      path = EnsemblRest.build_path "/info/comparas", opts
+
+      if opts['content-type'] == 'ruby'
+        plain_opts = opts.clone
+        plain_opts['content-type'] = 'application/json'
+        return JSON.parse info_comparas plain_opts
+      end
+
+      return EnsemblRest.fetch_data path, opts, 'information'      
+    end
+
+
+    ##
+    # Shows the data releases available on this REST server
+    def self.info_data(opts = {})
+      opts = EnsemblRest.parse_options opts
+      path = EnsemblRest.build_path "/info/data", opts
+
+      if opts['content-type'] == 'ruby'
+        plain_opts = opts.clone
+        plain_opts['content-type'] = 'application/json'
+        return JSON.parse info_data plain_opts
+      end
+
+      return EnsemblRest.fetch_data path, opts, 'information'      
+    end   
+
+
+    ##
+    # Pings the first available DBAdaptor to see if the service is still active
+    def self.info_ping(opts = {})
+      opts = EnsemblRest.parse_options opts
+      path = EnsemblRest.build_path "/info/ping", opts
+
+      if opts['content-type'] == 'ruby'
+        plain_opts = opts.clone
+        plain_opts['content-type'] = 'application/json'
+        return JSON.parse info_ping plain_opts
+      end
+
+      return EnsemblRest.fetch_data path, opts, 'information' 
+    end
+
+
+    ##
+    # Shows the current version of the REST API
+     def self.info_rest(opts = {})
+      opts = EnsemblRest.parse_options opts
+      path = EnsemblRest.build_path "/info/rest", opts
+
+      if opts['content-type'] == 'ruby'
+        plain_opts = opts.clone
+        plain_opts['content-type'] = 'application/json'
+        return JSON.parse info_rest plain_opts
+      end
+
+      return EnsemblRest.fetch_data path, opts, 'information' 
+    end   
+
+
+    ##
+    # Shows the current version of the Ensembl API
+     def self.info_software(opts = {})
+      opts = EnsemblRest.parse_options opts
+      path = EnsemblRest.build_path "/info/software", opts
+
+      if opts['content-type'] == 'ruby'
+        plain_opts = opts.clone
+        plain_opts['content-type'] = 'application/json'
+        return JSON.parse info_software plain_opts
+      end
+
+      return EnsemblRest.fetch_data path, opts, 'information' 
+    end  
+
+
+    ##
+    # Lists all available species, their aliases, available adaptor groups and data release
+     def self.info_species(opts = {})
+      opts = EnsemblRest.parse_options opts
+      path = EnsemblRest.build_path "/info/species", opts
+
+      if opts['content-type'] == 'ruby'
+        plain_opts = opts.clone
+        plain_opts['content-type'] = 'application/json'
+        return JSON.parse info_species plain_opts
+      end
+
+      return EnsemblRest.fetch_data path, opts, 'information' 
+    end 
+
+
+  end
+end

data/lib/bio-ensembl-rest/lookup.rb

@@ -0,0 +1,20 @@
+module EnsemblRest
+  module Lookup
+
+    ##
+    # Query for an identifier's location in the available Ensembl databases
+    def self.lookup_id(id, opts = {})
+      opts = EnsemblRest.parse_options opts
+      path = EnsemblRest.build_path "/lookup/id/#{id}", opts
+
+      if opts['content-type'] == 'ruby'
+        plain_opts = opts.clone
+        plain_opts['content-type'] = 'application/json'
+        return JSON.parse lookup_id id, plain_opts
+      end
+
+      return EnsemblRest.fetch_data path, opts, 'lookup' 
+    end
+
+  end
+end

data/lib/bio-ensembl-rest/mapping.rb

@@ -0,0 +1,55 @@
+module EnsemblRest
+  module Mapping
+
+    ##
+    # Convert the co-ordinates of one assembly to another
+    def self.map(asm_one, asm_two, species, region, opts = {})
+      opts = EnsemblRest.parse_options opts
+      path = EnsemblRest.build_path "/map/#{species}/#{asm_one}/#{region}/#{asm_two}", opts
+
+      # TODO: ruby object?
+      if opts['content-type'] == 'ruby'
+        plain_opts = opts.clone
+        plain_opts['content-type'] = 'application/json'
+        return JSON.parse map asm_one, asm_two, species, region, plain_opts
+      end
+
+      return EnsemblRest.fetch_data path, opts, 'mapping' 
+    end
+
+
+    ##
+    # Convert from CDNA coordinates to genomic coordinates
+    def self.map_from_cdna(id, region, opts = {})
+      return _map_generic id, region, 'cdna', opts       
+    end
+
+    ##
+    # Convert from CDS coordinates to genomic coordinates
+    def self.map_from_cds(id, region, opts = {})
+      return _map_generic id, region, 'cds', opts
+    end
+
+    ##
+    # Convert from protein (translation) coordinates to genomic coordinates
+    def self.map_from_translation(id, region, opts = {})
+      return _map_generic id, region, 'translation', opts
+    end
+
+    # generic mapping from cdna and cds
+    def self._map_generic(id, region, type, opts = {}) # :nodoc:
+      opts = EnsemblRest.parse_options opts
+      path = EnsemblRest.build_path "/map/#{type}/#{id}/#{region}", opts
+
+      # TODO: ruby object?
+      if opts['content-type'] == 'ruby'
+        plain_opts = opts.clone
+        plain_opts['content-type'] = 'application/json'
+        return JSON.parse _map_generic id, region, type, plain_opts
+      end
+
+      return EnsemblRest.fetch_data path, opts, 'mapping'
+    end
+
+  end
+end

data/lib/bio-ensembl-rest/ontologies.rb

@@ -0,0 +1,68 @@
+module EnsemblRest
+  module Ontologies
+
+    ##
+    # Find all ancestors, all terms above, belonging to a given term
+    def self.ontology_ancestor(id, opts = {})
+      return _ontology_id_generic id, 'ancestors_plain', opts
+    end
+
+    ##
+    # Reconstruct the entire ancestory of a term from is_a and part_of relationships.
+    def self.ontology_ancestor_chart(id, opts = {})
+      return _ontology_id_generic id, 'ancestors_chart', opts
+    end 
+
+    ##
+    # Find all descendents, all terms below, belonging to a given term. 
+    def self.ontology_descendents(id, opts = {})
+      return _ontology_id_generic id, 'descendents', opts
+    end
+
+    ##
+    # Search for an ontological term by its namespaced identifier
+    def self.ontology_id(id, opts = {})
+      return _ontology_id_generic id, 'plain', opts
+    end
+
+    def self._ontology_id_generic(id, type, opts = {}) # :nodoc:
+      opts = EnsemblRest.parse_options opts
+      case type 
+      when 'ancestors_plain'
+        url = "/ontology/ancestors/#{id}"
+      when 'ancestors_chart'
+        url = "/ontology/ancestors/chart/#{id}"
+      when 'descendents'
+        url = "/ontology/descendents/#{id}"
+      when 'plain'
+        url = "/ontology/id/#{id}"
+      end
+      path = EnsemblRest.build_path url, opts
+
+      if opts['content-type'] == 'ruby'
+        plain_opts = opts.clone
+        plain_opts['content-type'] = 'application/json'
+        return JSON.parse _ontology_id_generic id, type, plain_opts
+      end
+
+      return EnsemblRest.fetch_data path, opts, 'ontologies'
+    end
+
+
+    ##
+    # Search for a list of ontological terms by their name and an optional ontology
+    def self.ontology_name(name, opts = {})
+      opts = EnsemblRest.parse_options opts
+      path = EnsemblRest.build_path "/ontology/name/#{name}", opts
+      
+      if opts['content-type'] == 'ruby'
+        plain_opts = opts.clone
+        plain_opts['content-type'] = 'application/json'
+        return JSON.parse ontology_name name, plain_opts
+      end
+
+      return EnsemblRest.fetch_data path, opts, 'ontologies'
+    end
+
+  end
+end

data/lib/bio-ensembl-rest/sequence.rb

@@ -0,0 +1,37 @@
+module EnsemblRest
+  module Sequence
+
+    ##
+    # Query for multiple types of Sequence by its stable identifier
+    def self.sequence_id(id, opts = {}) 
+      opts = EnsemblRest.parse_options opts
+      path = EnsemblRest.build_path "/sequence/id/#{id}", opts
+
+      # FIXME: if multiseq is true Bio::Sequence can't parse text/plain right
+      if opts['content-type'] == 'ruby'
+        plain_opts = opts.clone
+        plain_opts['content-type'] = 'text/plain'
+        return Bio::Sequence.auto(sequence_id(id, plain_opts))
+      end
+
+      return EnsemblRest.fetch_data path, opts, 'sequence'
+    end
+
+
+    ##
+    # Query for a region of genomic sequence based on its location
+    def self.sequence_region(species, region, opts = {})
+      opts = EnsemblRest.parse_options opts
+      path = EnsemblRest.build_path "/sequence/region/#{species}/#{region}", opts
+
+      if opts['content-type'] == 'ruby'
+        plain_opts = opts.clone
+        plain_opts['content-type'] = 'text/plain'
+        return Bio::Sequence.auto sequence_region(species, region, plain_opts)
+      end
+
+      return EnsemblRest.fetch_data path, opts,  'sequence'
+    end
+
+  end
+end

data/lib/bio-ensembl-rest/taxonomy.rb

@@ -0,0 +1,30 @@
+module EnsemblRest
+  module Taxonomy
+
+    ##
+    # Search for a taxonomic term by its identifier or name
+    def self.taxonomy_id(id, opts = {})
+      return _taxonomy_generic id, 'id', opts
+    end
+
+    ##
+    # Return the taxonomic classification of a taxon node
+    def self.taxonomy_classification(id, opts = {})
+      return _taxonomy_generic id, 'classification', opts
+    end
+
+    def self._taxonomy_generic(id, type, opts = {}) # :nodoc:
+      opts = EnsemblRest.parse_options opts
+      path = EnsemblRest.build_path "/taxonomy/#{type}/#{id}", opts
+
+      if opts['content-type'] == 'ruby'
+        plain_opts = opts.clone
+        plain_opts['content-type'] = 'application/json'
+        return JSON.parse _taxonomy_generic id, type, plain_opts
+      end
+
+      return EnsemblRest.fetch_data path, opts, 'taxonomy'
+    end
+
+  end
+end

data/lib/bio-ensembl-rest/variation.rb

@@ -0,0 +1,37 @@
+module EnsemblRest
+  module Variation
+
+    ##
+    # Fetch variant consequences based on a variation identifier
+    def self.vep_id(id, species, opts = {})
+      opts = EnsemblRest.parse_options opts
+      path = EnsemblRest.build_path "/vep/#{species}/id/#{id}/consequences", opts
+
+      if opts['content-type'] == 'ruby'
+        plain_opts = opts.clone
+        plain_opts['content-type'] = 'application/json'
+        return JSON.parse vep_id id, species, plain_opts
+      end
+
+      return EnsemblRest.fetch_data path, opts, 'variation'
+    end
+
+
+    ##
+    # Fetch variant consequences
+    def self.vep_region(allele, region, species, opts = {})
+      opts = EnsemblRest.parse_options opts
+      path = EnsemblRest.build_path "/vep/#{species}/#{region}/#{allele}/consequences", opts
+
+      # TODO: ruby object?
+      if opts['content-type'] == 'ruby'
+        plain_opts = opts.clone
+        plain_opts['content-type'] = 'application/json'
+        return JSON.parse vep_region allele, region, species, plain_opts
+      end
+
+      return EnsemblRest.fetch_data path, opts, 'taxonomy'
+    end
+
+  end
+end

data/test/helper.rb

@@ -0,0 +1,20 @@
+require 'rubygems'
+require 'bundler'
+
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+
+require 'test/unit'
+require 'shoulda'
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+
+require 'bio-ensembl-rest'
+include EnsemblRest
+