idclight 0.1.1 → 0.1.2

data/VERSION

@@ -1 +1 @@
-0.1.1
+0.1.2

data/bin/convert.rb

@@ -19,12 +19,12 @@ if ARGV.length >= 2 and ARGV.length <= 3
 	id_type = ARGV[0]
 	id = ARGV[1]
 	org = ARGV[2] unless ARGV[2].nil?
-	r = convert(id_type, id, org)
+	r = search(id_type, id, org)
 	if r.nil?
 	  puts "No result. Bad input, perhaps? :/"
 	  code = 1
 	else
-		puts "\n"
+		puts r
 	end
 else
 	puts "\n\tUsage: #{__FILE__} <id_type> <id> [organism (defaults to human)]"

data/bin/ensembl_to_entrez.rb

@@ -0,0 +1,32 @@
+#!/usr/bin/env ruby
+
+current_dir = File.dirname(File.expand_path(__FILE__))
+lib_path = File.join(current_dir, '..', 'lib')
+$LOAD_PATH.unshift lib_path
+
+require 'rubygems'
+
+require 'idclight'
+
+include IDConverter::Light
+
+
+code = 0
+puts "\n"
+puts "IDCLight (IDConverter Light) command-line converter utility, by Preston Lee. (Screen scapes http://idclight.bioinfo.cnio.es for data.)"
+if ARGV.length == 1
+	id = ARGV[0]
+	r = ensembl_id_to_entrez_id(id)
+	if r.nil?
+	  puts "No result. Bad input, perhaps? :("
+	  code = 1
+	else
+		puts "\n#{r}"
+	end
+else
+	puts "\n\tUsage: #{__FILE__} <id>"
+end
+puts "\n"
+
+exit(code)
+

data/bin/ensembl_to_hugo.rb

@@ -0,0 +1,32 @@
+#!/usr/bin/env ruby
+
+current_dir = File.dirname(File.expand_path(__FILE__))
+lib_path = File.join(current_dir, '..', 'lib')
+$LOAD_PATH.unshift lib_path
+
+require 'rubygems'
+
+require 'idclight'
+
+include IDConverter::Light
+
+
+code = 0
+puts "\n"
+puts "IDCLight (IDConverter Light) command-line converter utility, by Preston Lee. (Screen scapes http://idclight.bioinfo.cnio.es for data.)"
+if ARGV.length == 1
+	id = ARGV[0]
+	r = ensembl_id_to_hugo_id(id)
+	if r.nil?
+	  puts "No result. Bad input, perhaps? :("
+	  code = 1
+	else
+		puts "\n#{r}"
+	end
+else
+	puts "\n\tUsage: #{__FILE__} <id>"
+end
+puts "\n"
+
+exit(code)
+

data/bin/hugo_to_ensembl.rb

@@ -0,0 +1,32 @@
+#!/usr/bin/env ruby
+
+current_dir = File.dirname(File.expand_path(__FILE__))
+lib_path = File.join(current_dir, '..', 'lib')
+$LOAD_PATH.unshift lib_path
+
+require 'rubygems'
+
+require 'idclight'
+
+include IDConverter::Light
+
+
+code = 0
+puts "\n"
+puts "IDCLight (IDConverter Light) command-line converter utility, by Preston Lee. (Screen scapes http://idclight.bioinfo.cnio.es for data.)"
+if ARGV.length == 1
+	id = ARGV[0]
+	r = hugo_id_to_ensembl_id(id)
+	if r.nil?
+	  puts "No result. Bad input, perhaps? :("
+	  code = 1
+	else
+		puts "\n#{r}"
+	end
+else
+	puts "\n\tUsage: #{__FILE__} <id>"
+end
+puts "\n"
+
+exit(code)
+

data/bin/hugo_to_entrez.rb

@@ -24,7 +24,7 @@ if ARGV.length == 1
 		puts "\n#{r}"
 	end
 else
-	puts "\n\tUsage: #{__FILE__} <id_type> <id> [organism (defaults to human)]"
+	puts "\n\tUsage: #{__FILE__} <id>"
 end
 puts "\n"
 

data/idclight.gemspec

@@ -5,14 +5,14 @@
 
 Gem::Specification.new do |s|
   s.name = %q{idclight}
-  s.version = "0.1.1"
+  s.version = "0.1.2"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Preston Lee"]
-  s.date = %q{2010-05-10}
+  s.date = %q{2010-05-11}
   s.description = %q{A Ruby gem for accessing the freely available IDClight (IDConverter Light) web service, which convert between different types of gene IDs such as Hugo and Entrez. Queries are screen scraped from http://idclight.bioinfo.cnio.es.}
   s.email = %q{conmotto@gmail.com}
-  s.executables = ["convert.rb", "hugo_to_entrez.rb"]
+  s.executables = ["convert.rb", "ensembl_to_entrez.rb", "ensembl_to_hugo.rb", "hugo_to_ensembl.rb", "hugo_to_entrez.rb"]
   s.extra_rdoc_files = [
     "LICENSE",
      "README.rdoc"
@@ -26,6 +26,9 @@ Gem::Specification.new do |s|
      "Rakefile",
      "VERSION",
      "bin/convert.rb",
+     "bin/ensembl_to_entrez.rb",
+     "bin/ensembl_to_hugo.rb",
+     "bin/hugo_to_ensembl.rb",
      "bin/hugo_to_entrez.rb",
      "idclight.gemspec",
      "lib/idclight.rb",

data/lib/idclight.rb

@@ -15,7 +15,7 @@ module IDConverter
     # ID type constants.
     @@UNIGENE		= 'ug'
     @@ENTREZ		= 'entrez'
-    @@ENSEMBL		= 'ensumbl'
+    @@ENSEMBL		= 'ensembl'
     @@HUGO			= 'hugo'
     @@GENBANK		= 'acc'
     @@CLONE			= 'clone'
@@ -68,17 +68,58 @@ module IDConverter
     
     def hugo_id_to_entrez_id(id, organism = @@HUMAN)
       data = search(@@HUGO, id, organism)
-      id = nil
-      ent = data['Entrez Gene']
-      if ent
-        doc = Hpricot(ent)
-        doc.search('//a').each do |e|
-          tmp = e.inner_html.to_i
-          id = tmp if tmp != 0 
-        end
-      end
-      id
+      extract_entrez_id(data)
+    end
+
+    def hugo_id_to_ensembl_id(id, organism = @@HUMAN)
+      data = search(@@HUGO, id, organism)
+      extract_ensembl_id(data)
+    end
+
+    def ensembl_id_to_entrez_id(id, organism = @@HUMAN)
+     	data = search(@@ENSEMBL, id, organism)
+ 		extract_entrez_id(data)
+    end
+
+    def ensembl_id_to_hugo_id(id, organism = @@HUMAN)
+     	data = search(@@ENSEMBL, id, organism)
+ 		extract_hugo_id(data)
     end
+
+	def extract_entrez_id(data)
+		ent = data['Entrez Gene']
+		id = nil
+		if ent
+			doc = Hpricot(ent)
+	        doc.search('//a').each do |e|
+	          tmp = e.inner_html.to_i
+	          id = tmp if tmp != 0 
+	        end
+		end	
+		id
+	end
+	
+	def extract_hugo_id(data)
+		ent = data['HUGO']
+		extract_last_link_text(ent)
+	end
+
+	def extract_ensembl_id(data)
+		ent = data['Ensembl']
+		extract_last_link_text(ent)
+	end
+
+	def extract_last_link_text(ent)
+		id = nil
+		if ent
+			doc = Hpricot(ent)
+	        doc.search('//a').each do |e|
+	          tmp = e.inner_html
+	          id = tmp if !tmp.nil? && tmp != ''
+	        end
+		end	
+		id
+	end
     
   end
   

metadata

@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
   segments: 
   - 0
   - 1
-  - 1
-  version: 0.1.1
+  - 2
+  version: 0.1.2
 platform: ruby
 authors: 
 - Preston Lee
@@ -14,7 +14,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-05-10 00:00:00 -07:00
+date: 2010-05-11 00:00:00 -07:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -46,6 +46,9 @@ description: A Ruby gem for accessing the freely available IDClight (IDConverter
 email: conmotto@gmail.com
 executables: 
 - convert.rb
+- ensembl_to_entrez.rb
+- ensembl_to_hugo.rb
+- hugo_to_ensembl.rb
 - hugo_to_entrez.rb
 extensions: []
 
@@ -61,6 +64,9 @@ files:
 - Rakefile
 - VERSION
 - bin/convert.rb
+- bin/ensembl_to_entrez.rb
+- bin/ensembl_to_hugo.rb
+- bin/hugo_to_ensembl.rb
 - bin/hugo_to_entrez.rb
 - idclight.gemspec
 - lib/idclight.rb