sylfy 0.0.1 → 0.0.2

checksums.yaml

@@ -1,7 +1,7 @@
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data/lib/sylfy/service/keggrest/conv.rb

@@ -0,0 +1,62 @@
+# 
+# UniSysDB library in Ruby
+# Copyright (C) 2012
+#
+# @author Natapol Pornputtapong <natapol@chalmers.se>
+#
+
+module Sylfy
+	
+	module Service
+	
+		module KEGGREST
+			
+			module_function
+			
+			def conv(id, targetdb = nil)
+				
+				help = %Q(
+help:	conv(id, targetdb = nil)
+help:
+help:	
+help:	targetdb = <database>
+help:	For gene identifiers:
+help:	<kegg_db> = <org>
+help:	<org> = KEGG organism code or T number
+help:	<outside_db> = ncbi-gi | ncbi-geneid | uniprot
+help:
+help:	For chemical substance identifiers:
+help:	<kegg_db> = drug | compound | glycan
+help:	<outside_db> = pubchem | chebi
+help:	
+help:	return a Hash
+				)
+				if id == :help
+					puts help
+					return {}
+				else
+					
+					begin
+						doc = URI.parse("#{@@baseuri}/conv/#{targetdb}/#{id}").read().strip()
+						result = {}
+						
+						doc.split(/\n/).each do |line|
+							dat = line.chomp.split(/\t/)
+							result[dat[0]] = [] if !result.has_key?(dat[0])
+							result[dat[0]].push(dat[1])
+						end
+						
+						return result
+						
+					rescue OpenURI::HTTPError
+						raise Sylfy::Service::DataNotFound, "Query not found."
+					end
+					
+				end
+			end
+		
+		end
+		
+	end
+	
+end

data/lib/sylfy/service/keggrest/find.rb

@@ -0,0 +1,89 @@
+# 
+# UniSysDB library in Ruby
+# Copyright (C) 2012
+#
+# @author Natapol Pornputtapong <natapol@chalmers.se>
+#
+
+module Sylfy
+	
+	module Service
+	
+		module KEGGREST
+			
+			module_function
+			# Method for setting inchi data member
+			#
+			# == Parameters:
+			# inchi::
+			#   input inchi string
+			def find(database, query=nil, option=nil)
+				
+				help = "
+help:	find(database, query, option=nil)
+help:
+help:	type#1
+help:	
+help:	database = <database>
+help:	<database> = pathway | module | disease | drug | environ | ko | genome |
+help:		<org> | compound | glycan | reaction | rpair | rclass | enzyme |
+help:		genes | ligand
+help:	<org> = KEGG organism code or T number
+help:	
+help:	<option> = formula | exact_mass | mol_weight only for <database> = compound | drug
+help:	
+help:	return a List
+				"
+				
+				result_tag = {
+					:pathway => [:NAME],
+					:module => [:NAME],
+					:disease => [:NAME],
+					:drug => [:NAME],
+					:environ => [:NAME],
+					:ko => [:NAME, :DEFINITION],
+					:genome => [:NAME, :DEFINITION],
+					:compound => [:NAME],
+					:glycan => [:NAME, :COMPOSITION, :CLASS],
+					:reaction => [:NAME, :DEFINITION],
+					:rpair => [:NAME],
+					:rclass => [:NAME, :DEFINITION],
+					:enzyme => [:NAME]
+				}
+				result_tag.default = [:NAME, :DEFINITION, :ORTHOLOGY]
+				result = {}
+				if database == :help
+					puts help
+					return result
+				else
+					begin
+						if ['compound', 'drug'].include?(database.to_s) && option != nil &&
+							['formula', 'exact_mass' 'mol_weight'].include?(option.to_s)
+							URI.parse("#{@@baseuri}/find/#{database}/#{query}/#{option}").read().strip().each do |line|
+								dat = line.chomp.split(/\t/)
+								result[dat[0]] = { option.to_sym => dat[1]}
+							end
+						else
+							URI.parse("#{@@baseuri}/find/#{database}/#{query}").read().strip().each do |line|
+								dat = line.chomp.split(/\t/)
+								result[dat[0]] = {}
+								info = dat[1].split('; ')
+								info.each_index {|ind| result[dat[0]][result_tag[database.to_sym][ind]] = info[ind]}
+							end
+						end
+						
+						return result
+					rescue OpenURI::HTTPError
+						raise Unisys::ServiceException, "Query not found."
+					end
+				
+				end
+				
+			end
+		
+		end
+		
+	end
+	
+end
+

data/lib/sylfy/service/keggrest/link.rb

@@ -0,0 +1,61 @@
+# 
+# UniSysDB library in Ruby
+# Copyright (C) 2012
+#
+# @author Natapol Pornputtapong <natapol@chalmers.se>
+#
+
+module Sylfy
+	
+	module Service
+	
+		module KEGGREST
+			
+			module_function
+			# Method for setting inchi data member
+			#
+			# == Parameters:
+			# inchi::
+			#   input inchi string
+			def link(id, targetdb = nil)
+				
+				help = "
+help:	link(id, targetdb = nil)
+help:
+help:	targetdb = pathway | brite | module | disease | drug | environ | ko | genome | <org> | compound | glycan | reaction | rpair | rclass | enzyme
+help:
+help:	id = KEGG database entries involving the following databases: pathway | brite | module | disease | drug | environ | ko | genome |
+help:		<org> | compound | glycan | reaction | rpair | rclass | enzyme
+help:	<org> = KEGG organism code or T number
+help:
+help:	<option> = aaseq | ntseq | mol | kcf | image
+				"
+				if id == :help
+					puts help
+					return {}
+				else
+					
+					begin
+						doc = URI.parse("#{@@baseuri}/link/#{targetdb}/#{id}").read().strip()
+						result = {}
+						
+						doc.each do |line|
+							dat = line.chomp.split(/\t/)
+							result[dat[0]] = result.has_key?(dat[0]) ? result[dat[0]].push(dat[1]) : [dat[1]]
+						end
+					
+						return result
+					rescue OpenURI::HTTPError
+						raise Sylfy::Service::DataNotFound, "Query not found."
+					end
+				
+					
+				end
+				
+			end
+		
+		end
+		
+	end
+	
+end

data/lib/sylfy/service/keggrest/list.rb

@@ -0,0 +1,72 @@
+# 
+# UniSysDB library in Ruby
+# Copyright (C) 2012
+#
+# @author Natapol Pornputtapong <natapol@chalmers.se>
+#
+
+module Sylfy
+	
+	module Service
+		
+		module KEGGREST
+			
+			module_function
+			
+			def list(param)
+				
+				help = %Q(
+help:	list(param)
+help:
+help:	type#1
+help:	
+help:	param = \"<database>\"
+help:	<database> = pathway | brite | module | disease | drug | environ | ko | genome |
+help:					<org> | compound | glycan | reaction | rpair | rclass | enzyme | organism
+help:	
+help:	<org> = KEGG organism code or T number
+help:	
+help:	
+help:	type#2
+help:	
+help:	param = \"<database>/<org>\"
+help:	<database> = pathway | module
+help:	<org> = KEGG organism code
+help:	
+help:	type#3
+help:	
+help:	param = \"<dbentries>\"
+help:	<dbentries> = KEGG database entries involving the following databases: pathway | brite | module | disease | drug | environ | ko | genome |
+help:					<org> | compound | glycan | reaction | rpair | rclass | enzyme | organism
+help:	
+help:	return a List
+				)
+				
+				if param == :help
+					puts help
+					return {}
+				else
+					
+					begin
+						doc = URI.parse("#{@@baseuri}/list/#{param.to_s}").read().strip()
+						result = {}
+						
+						doc.each do |line|
+							dat = line.chomp.split(/\t/, 2)
+							result[dat[0]] = dat[1]
+						end
+						
+						return result
+					rescue OpenURI::HTTPError
+						raise Sylfy::Service::DataNotFound, "Data not found."
+					end
+					
+				end
+				
+			end
+			
+		end
+	end
+	
+end
+

data/lib/sylfy/service/keggrest/restKegg_get.rb

@@ -0,0 +1,130 @@
+# 
+# UniSysDB library in Ruby
+# Copyright (C) 2012
+#
+# @author Natapol Pornputtapong <natapol@chalmers.se>
+#
+require 'open-uri'
+require 'net/http'
+require 'rexml/document'
+
+module Unisys
+	
+	module Service
+	
+		module RESTKegg
+			
+			module_function
+			
+			def get(id, option = nil)
+				
+				help = "
+help:	get(id, targetdb = nil)
+help:
+help:	<dbentries> = KEGG database entries involving the following databases: pathway | brite | module | disease | drug | environ | ko | genome |
+help:		<org> | compound | glycan | reaction | rpair | rclass | enzyme
+help:	<org> = KEGG organism code or T number
+help:
+help:	<option> = aaseq | ntseq | mol | kcf | image
+				"
+				if id == :help
+					puts help
+					return []
+				else
+					
+					if option != nil && ['aaseq', 'ntseq', 'mol', 'kcf', 'image'].include?(option.to_s)
+						text = "#{id}/#{option}"
+					else
+						text = "#{id}"
+					end
+					
+					begin
+						doc = URI.parse("#{@@baseuri}/get/#{text}").read().strip()
+						
+					rescue OpenURI::HTTPError
+						raise Unisys::ServiceException, "Query not found."
+					end
+					
+					doc = "\n\n\n#{doc}" if option != nil && option.to_sym == :mol
+					
+					return doc
+				end
+				
+			end
+			
+			def getSmallMolecule(id)
+				#:id, :dataPrimarySource, :xrefs, :relations :inchi, :formula, :smiles, :inchiKey :names :relatype :terminal
+				doc = get(id)
+				
+				rel_conv = {"Same as" => 'obo.internal:is_a'}
+				ref_conv = {"PubChem:" => "urn:miriam:pubchem.substance:", "ChEBI:" => "urn:miriam:obo.chebi:", "CAS:" => "urn:miriam:cas:", "3DMET:" => "urn:miriam:3dmet:", "KNApSAcK:" => "urn:miriam:knapsack:", "PDB-CCD:" => "urn:miriam:pdb-ccd:", "DrugBank:" => "urn:miriam:drugbank:", "LIPIDMAPS:" => "urn:miriam:lipidmaps:", "LipidBank:" => "urn:miriam:lipidbank:", "GlycomeDB:" => "urn:miriam:glycomedb:" }
+				
+				result = {}
+				result[:names] = []
+				result[:xrefs] = []
+				result[:relations] = []
+				
+				field = ""
+				content = ""
+				doc.split(/\n/).each do |line|
+					
+					if line =~ /^(\p{Upper}+) +(.*)/
+						field = $1.to_sym
+						content = $2.chomp
+					elsif line =~ /^ +(.*)/
+						content = $1.chomp
+					end
+					
+					case field
+					when :ENTRY
+						dat = content.split(/ +/)
+						result[:dataPrimarySource] = "#{Unisys::kegg_miriam[dat[0][0]]}:#{dat[0]}"
+					when :NAME
+						result[:names].push(content[0..-2])
+					when :FORMULA
+						result[:formula] = content
+					when :COMPOSITION
+						result[:formula] = content
+					when :MASS
+						
+					when :CLASS
+						
+					when :REMARK
+						dat = content.split(/: /)
+						
+						result[:relations].push({:relatype => rel_conv[dat[0]]}, :terminal => "#{Unisys::kegg_miriam[dat[1][0]]}:#{dat[1]}")
+					when :REFERENCE
+						
+						
+					when :REACTION
+						
+					when :PATHWAY
+						
+					when :ENZYME
+						
+					when :ORTHOLOGY
+						
+					when :DBLINKS
+						dat = content.split(/ /)
+						if ref_conv.has_key?(dat[0])
+							dat[1..-1].each do |item|
+								result[:xrefs].push("#{ref_conv[dat[0]]}#{item}")
+							end
+						end
+					when :NODE
+						
+					when :EDGE
+						
+					end
+					
+					#result.push(line.chomp.split(/\t/))
+				end
+				
+				return result
+			end
+		
+		end
+		
+	end
+	
+end

data/lib/sylfy/service/keggrest.rb

@@ -0,0 +1,50 @@
+# 
+# UniSysDB library in Ruby
+# Copyright (C) 2012
+#
+# @author Natapol Pornputtapong <natapol@chalmers.se>
+#
+require 'open-uri'
+require 'net/http'
+require 'rexml/document'
+
+
+require 'sylfy/service/keggrest/conv'
+require 'sylfy/service/keggrest/find'
+require 'sylfy/service/keggrest/link'
+require 'sylfy/service/keggrest/list'
+
+module Sylfy
+	
+	module Service
+		
+		
+		# http://rest.kegg.jp/<operation>/<argument>/<argument2 or option>
+		# <operation> = info | list | find | get | conv | link
+		# <argument> = <database> | <dbentries>
+		
+		module KEGGREST
+			
+			@@baseuri = "http://rest.kegg.jp"
+			
+			@@db = [:pathway, :brite, :module, :disease, :drug, :environ, 
+					:ko, :genome, :compound, :glycan, :reaction, :rpair, 
+					:rclass, :enzyme, :genomes, :genes, :ligand, :kegg, :organism]
+			
+			module_function
+			
+			
+		end
+		
+	end
+end
+
+#require '../unisys.rb'
+
+#p Unisys::Service::RESTKegg.list('hsa:10458+ece:Z5100')
+#p Unisys::Service::RESTKegg.find(:genes, 'shiga+toxin')
+#p Unisys::Service::RESTKegg.conv('hsa:10458+ece:Z5100','ncbi-gi')
+#p Unisys::Service::RESTKegg.get(:G00092)
+#Unisys::Service::RESTKegg.getSmallMolecule(:G00092)
+#p Unisys::Service::RESTKegg.link('hsa:10458+ece:Z5100', 'pathway')
+

data/lib/sylfy/version.rb

@@ -8,5 +8,5 @@
 #
 
 module Sylfy
-    VERSION = "0.0.1"
+    VERSION = "0.0.2"
 end

data/sylfy.gemspec

@@ -8,15 +8,15 @@ Gem::Specification.new do |s|
     s.date          = '2010-04-28'
     s.platform      = Gem::Platform::RUBY
     
-    s.summary       = ""
-    s.description   = "A simple hello world gem"
+    s.summary       = "Provides some useful functions for systems biology field."
+    s.description   = "Systems Biology Library for Ruby"
     s.authors       = ["Natapol Pornputtapong"]
     s.email         = 'natapol.por@gmail.com'
 
-    s.homepage      = 'http://rubygems.org/gems/hola'
+    s.homepage      = 'http://rubygems.org/gems/sylfy'
     s.license       = 'GPL'
     
-    s.rubyforge_project = "neography"
+#    s.rubyforge_project = "neography"
     
     s.files         = `git ls-files`.split("\n")
     s.test_files    = `git ls-files -- {test,spec,features}/*`.split("\n")
@@ -24,6 +24,7 @@ Gem::Specification.new do |s|
     s.require_paths = ["lib"]
     
     s.add_dependency "gsl", ">= 1.15.3"
+    s.add_dependency "bio", ">= 1.4.3.0001"
     
 #    s.add_development_dependency "rspec", ">= 2.11"
 #    s.add_development_dependency "net-http-spy", "0.2.1"

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: sylfy
 version: !ruby/object:Gem::Version
-  version: 0.0.1
+  version: 0.0.2
 platform: ruby
 authors:
 - Natapol Pornputtapong
@@ -24,7 +24,21 @@ dependencies:
     - - '>='
       - !ruby/object:Gem::Version
         version: 1.15.3
-description: A simple hello world gem
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.3.0001
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.3.0001
+description: Systems Biology Library for Ruby
 email: natapol.por@gmail.com
 executables: []
 extensions: []
@@ -33,9 +47,15 @@ files:
 - README.md
 - lib/sylfy.rb
 - lib/sylfy/math.rb
+- lib/sylfy/service/keggrest.rb
+- lib/sylfy/service/keggrest/conv.rb
+- lib/sylfy/service/keggrest/find.rb
+- lib/sylfy/service/keggrest/link.rb
+- lib/sylfy/service/keggrest/list.rb
+- lib/sylfy/service/keggrest/restKegg_get.rb
 - lib/sylfy/version.rb
 - sylfy.gemspec
-homepage: http://rubygems.org/gems/hola
+homepage: http://rubygems.org/gems/sylfy
 licenses:
 - GPL
 metadata: {}
@@ -54,9 +74,9 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: neography
+rubyforge_project: 
 rubygems_version: 2.0.3
 signing_key: 
 specification_version: 4
-summary: ''
+summary: Provides some useful functions for systems biology field.
 test_files: []