sylfy 0.0.2 → 0.1.0

data/lib/sylfy/math.rb

@@ -1,24 +0,0 @@
-# 
-# UniSysDB library in Ruby
-# Copyright (C) 2012
-#
-# author: Natapol Pornputtapong <natapol@chalmers.se>
-#
-# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
-#
-
-module Sylfy
-    
-    module Mathf
-        
-        def self.lnfactorial(n)
-            return GSL::Sf::lngamma(n+1)
-        end
-        
-        def self.hypergeomatrix_test(nn, m, n, k)
-            log_h = lnfactorial(m) - lnfactorial(k) - lnfactorial(m-k) + lnfactorial(nn-m) - lnfactorial(n-k) - lnfactorial(nn-m-n+k) - lnfactorial(nn) + lnfactorial(n) + lnfactorial(nn-n)
-            return (Math::E ** log_h)
-        end
-        
-    end
-end

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

@@ -1,130 +0,0 @@
-# 
-# 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