sylfy 0.0.2 → 0.1.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/README.md

@@ -1,2 +1,4 @@
 sylfy
 =====
+
+<a rel="license" href="http://creativecommons.org/licenses/by-nc-sa/3.0/deed.en_US"><img alt="Creative Commons License" style="border-width:0" src="http://i.creativecommons.org/l/by-nc-sa/3.0/88x31.png" /></a><br />This work is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by-nc-sa/3.0/deed.en_US">Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License</a>.

data/Rakefile

@@ -0,0 +1,13 @@
+require 'rake/testtask'
+require 'yard'
+
+Rake::TestTask.new do |t|
+    t.libs << 'test'
+end
+
+YARD::Rake::YardocTask.new do |t|
+  t.files   = ['lib/**/*.rb', '-']
+end
+
+#desc "Run tests"
+#task :default => :test

data/lib/sylfy.rb

@@ -1,6 +1,6 @@
 # 
-# UniSysDB library in Ruby
-# Copyright (C) 2012
+# Systems biology library for Ruby (Sylfy)
+# Copyright (C) 2012-2013
 #
 # author: Natapol Pornputtapong <natapol@chalmers.se>
 #
@@ -9,35 +9,22 @@
 
 # raise "Please, use ruby 1.9.0 or later." if RUBY_VERSION < "1.9.0"
 
-# == Overview
-#
-# 
-#
-# == Introduction
-#
-# 
-#
-# == Queries
-#
-# 
-#
-# === Environmental Variables
-#
-# 
-#
-# === Parameters
-#
-# 
 
-$: << File.join(File.expand_path(File.dirname(__FILE__)))
 
-require 'gsl'
+$: << File.join(File.expand_path(File.dirname(__FILE__)))
 
+require 'csv'
 
+require 'bio'
 
-require 'sylfy/math'
+require 'sylfy/mathf'
+require 'sylfy/service'
+require 'sylfy/feature'
+require 'sylfy/add'
+require 'sylfy/utils'
+require 'sylfy/pattern'
 
 module Sylfy
 
 
-end
+end

data/lib/sylfy/add.rb

@@ -0,0 +1,10 @@
+# 
+# UniSysDB library in Ruby
+# Copyright (C) 2012
+#
+# author: Natapol Pornputtapong <natapol.por@gmail.com>
+#
+# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
+#
+
+require 'sylfy/add/bio_kegg_kgml'

data/lib/sylfy/add/bio_kegg_kgml.rb

@@ -0,0 +1,108 @@
+require 'open-uri'
+
+# additional module of bio ruby library
+module Bio
+# Class Bio::KEGG
+class KEGG
+    # Class Bio::KEGG::KGML
+    class KGML
+        # convert KGML to mjson (map json)
+        def to_mjson()
+            mjson = {:identifier => :id}
+            
+            # <pathway> attributes
+            mjson[:name] = @name
+            mjson[:org] = @org
+            mjson[:number] = @number
+            mjson[:title] = @title
+            mjson[:link] = @link
+            
+            
+            mjson[:image] = {}
+            mjson[:image][:source] = @image
+            
+            begin
+                dim = open(@image).read()[0x10..0x18].unpack('NN')
+                mjson[:image][:width] = dim[0]
+                mjson[:image][:height] = dim[1]
+            rescue
+                
+            end
+            
+            
+            # <entry> attributes
+            @entries.each do |entry|
+                entryinfo = {:id => entry.id, :entryname => entry.name, :link => entry.link, :entrytype => entry.type, :keggid => entry.names}
+              
+                entryinfo[:reaction] = entry.reaction if entry.reaction
+                
+                # <graphics> attributes
+                graphicinfo = {}
+                if entry.graphics.length == 1
+                    graphicinfo[:fill] = entry.graphics[0].bgcolor if entry.graphics[0].bgcolor
+                    graphicinfo[:stroke] = entry.graphics[0].fgcolor if entry.graphics[0].fgcolor
+                    graphicinfo[:name] = entry.graphics[0].name if entry.graphics[0].name
+            
+                    case entry.graphics[0].type
+                    when 'rectangle'
+                        graphicinfo[:type] = :rect
+                        graphicinfo[:width] = entry.graphics[0].width
+                        graphicinfo[:height] = entry.graphics[0].height
+                        graphicinfo[:x] = entry.graphics[0].x
+                        graphicinfo[:y] = entry.graphics[0].y
+                    when 'roundrectangle'
+                        graphicinfo[:type] = :rect
+                        graphicinfo[:width] = entry.graphics[0].width
+                        graphicinfo[:height] = entry.graphics[0].height
+                        graphicinfo[:x] = entry.graphics[0].x
+                        graphicinfo[:y] = entry.graphics[0].y
+                        graphicinfo[:r] = 10
+                    when 'circle'
+                        graphicinfo[:type] = :circle
+                        graphicinfo[:r] = entry.graphics[0].width/2
+                        graphicinfo[:cx] = entry.graphics[0].x
+                        graphicinfo[:cy] = entry.graphics[0].y
+                    when 'line'
+                        graphicinfo[:type] = :path
+                        paths = []
+                        entry.graphics[0].coords.each {|coord| paths.push(coord.join(" "))}
+                        graphicinfo[:fill] = entry.graphics[0].bgcolor if entry.graphics[0].bgcolor
+                        graphicinfo[:stroke] = entry.graphics[0].fgcolor if entry.graphics[0].fgcolor
+                        graphicinfo[:name] = entry.graphics[0].name if entry.graphics[0].name
+                        graphicinfo[:d] ||= ""
+                        graphicinfo[:d] += "M #{paths.join("L")}" if !paths.empty?()
+                        graphicinfo[:"stroke-width"] = 3
+                        graphicinfo[:"stroke-linecap"] = "square"
+                    end
+                    
+                else
+                    entry.graphics.each do |graph|
+                        if graph.type == 'line'
+                            paths = []
+                            graph.coords.each {|coord| paths.push(coord.join(" "))}
+                            graphicinfo[:type] = :path
+                            graphicinfo[:fill] = graph.bgcolor if graph.bgcolor
+                            graphicinfo[:stroke] = graph.fgcolor if graph.fgcolor
+                            graphicinfo[:name] = graph.name if graph.name
+                            graphicinfo[:d] ||= ""
+                            graphicinfo[:d] += "M #{paths.join("L")}" if !paths.empty?()
+                            graphicinfo[:"stroke-width"] = 3
+                            graphicinfo[:"stroke-linecap"] = "square"
+                        else
+                            raise "Graphic parsinf error to #{id}:#{entry.id}"
+                        end
+                    end
+                end
+                
+                entryinfo[:graphic] = graphicinfo
+                mjson[graphicinfo[:type]] ||= []
+                mjson[graphicinfo[:type]].push(entryinfo)
+            
+                # <component> attributes
+                
+            end
+            return mjson
+        end
+    end
+end
+end

data/lib/sylfy/datamodel.rb

@@ -0,0 +1,141 @@
+# author: Natapol Pornputtapong <natapol.por@gmail.com>
+#
+# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
+#
+require 'json'
+
+module Sylfy
+    # Model template
+    class DataModel
+        
+        class DuplicateError < Exception
+            
+        end
+        
+        attr_reader :data
+        # Initialize function
+        # @param data [Hash] data object
+        def initialize(data = nil)
+            @data = {class: self.class.to_sym}
+            if data
+                data.each_pair do |field, value|
+                    self.send "#{field}=".to_sym, value if self.method_defined?(field)
+                end
+            end
+            
+        end
+        
+        # convert data object to JSON
+        # @return [JSON]
+        def to_json()
+            return @data.to_json
+        end
+        # @return [String]
+        def to_str()
+            return JSON::pretty_generate(@data)
+        end
+        # @return [Hash]
+        def to_hash()
+            return @data
+        end
+        # Test if data object is valid
+        def valid?()
+            if @@validates
+                result = true
+                @@validates.each_pair do |field, rules|
+                    rules.each_pair do |type, rule|
+                        case type.to_sym
+                        when :type
+                            if rule.kind_of?(Array)
+                                rule.each {|e| result &&= self.assert_type_of?(e, @data[field.to_sym])}
+                            else
+                                result &&= self.assert_type_of?(rule, @data[field.to_sym])
+                            end
+                        when :presence
+                            result &&= !(rule ^ (@data[field.to_sym] != nil && !@data[field.to_sym].empty?))
+                        when :format
+                            if rule.kind_of?(Array)
+                                rule.each {|e| result &&= self.assert_match?(e, @data[field.to_sym])}
+                            else
+                                result &&= self.assert_match?(rule, @data[field.to_sym])
+                            end
+                        end
+                    end
+                end
+                return result
+            else
+                return true
+            end
+        end
+        
+        def assert_type_of?(crass, value)
+            if crass < DataModel
+                return crass.new(value).valid?
+            else
+                return value.kind_of?(crass)
+            end
+        end
+        
+        protected :assert_type_of?
+        
+        def assert_match?(pattern, value)
+            return value.kind_of?(String) && value =~ pattern ? true : false
+        end
+        
+        protected :assert_match?
+        
+        def self.has_one(*attrs)
+            @@has_one ||= []
+            attrs.each do |attr|
+                if !self.method_defined?(attr)
+                    @@has_one.push(attr)
+                    self.class_eval do
+                        define_method(attr) do
+                            @data[attr]
+                        end
+                        
+                        define_method("#{attr}=") do |param|
+                            @data[attr] = param.kind_of?(DataModel) ? param.to_hash : param
+                        end
+                    end
+                else
+                    raise DuplicateError, "#{attr.inspect} is already defined."
+                end
+            end
+        end
+        
+        def self.has_many(*attrs)
+            @@has_many ||= []
+            attrs.each do |attr|
+                if !self.method_defined?(attr)
+                    @@has_many.push(attr)
+                    self.class_eval do
+                        define_method(attr) do
+                            @data[attr] = []
+                        end
+                        
+                        define_method("#{attr}=") do |*param|
+                            @data[attr] = param.flatten
+                        end
+                        
+                        define_method("#{attr}_add") do |*param|
+                            @data[attr] += param.flatten
+                        end
+                    end
+                else
+                    raise DuplicateError, "#{attr.inspect} is already defined."
+                end
+            end
+        end
+        
+        def self.validates(*attrs, rules)
+            @@validates ||= {}
+            attrs.each do |attr|
+                @@validates[attr] ||= {}
+                @@validates[attr].merge!(rules)
+            end
+        end
+        
+        #class << self;self;end.send :protected, :subjects_xml, :subjects_html
+    end
+end

data/lib/sylfy/feature.rb

@@ -0,0 +1,128 @@
+# 
+# UniSysDB library in Ruby
+# Copyright (C) 2012
+#
+# author: Natapol Pornputtapong <natapol@chalmers.se>
+#
+# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
+#
+# This class is used by Ondine
+
+module Sylfy
+    
+    class Feature
+        
+        attr_reader :member, :listnumber, :length
+        
+        def initialize(listnumber, member, length)
+            @listnumber = listnumber
+            @member = member
+            @length = length
+        end
+        
+        protected :initialize
+        
+        def self.open(filename, options)
+            #@listnumber = {:path => { "path:map00010"=>["Glycolysis / Gluconeogenesis"], ...}, "gene" => {"path:map00010"=>["ko:K00001", "ko:K00002", ...], ...}, "comp" => {... }
+            #"ko:K02790"=>{"gene"=>["path:map00010", "path:map00500", "path:map02060"]}
+            listnumber = {}
+            member = {}
+            length = {}
+            # type group member
+            CSV.open(filename, "rb", options).readlines.each do |row|
+                length[row[0]] = 0 if !length.has_key?(row[0])
+                listnumber[row[0]] = {} if !listnumber.has_key?(row[0])
+                listnumber[row[0]][row[1]] = [] if !listnumber[row[0]].has_key?(row[1])
+                listnumber[row[0]][row[1]].push(row[2])
+                
+                if row[0] != 'path'
+                    if !member.has_key?(row[2]) && 
+                        member[row[2]] = {}
+                        member[row[2]].default = []
+                        length[row[0]] += 1
+                    end
+                    
+                    member[row[2]][row[0]] = [] if !member[row[2]].has_key?(row[0])
+                    member[row[2]][row[0]].push(row[1])
+                    
+                end
+            end
+            return Sylfy::Feature.new(listnumber, member, length)
+        end
+        
+        def self.fromKEGG(species = 'ref')
+            
+            listnumber = {}
+            member = {}
+            complist = Service::KEGGREST.link("compound/pathway")
+            
+            if species == 'ref'
+                pathwaylist = Service::KEGGREST.list("pathway")
+                genelist = Service::KEGGREST.link("ko/pathway")
+                genelist.delete_if{|k, v| k !~ /^path:map/ }
+                complist.delete_if{|k, v| k !~ /^path:map/ }
+                
+            else
+                pathwaylist = Service::KEGGREST.list("pathway/#{species}")
+                genelist = Service::KEGGREST.link("#{species}/pathway")
+                tmp = {}
+                complist.each_pair do |k, v|
+                    tmp["path:#{species}#{k[-6..-1]}"] = v if !tmp.has_key?("path:#{species}#{k[-6..-1]}")
+                end
+                complist = tmp
+            end
+            
+            listnumber["path"] = pathwaylist
+            listnumber["gene"] = genelist
+            listnumber["comp"] = complist
+            
+            length = {"path" => pathwaylist.length}
+            genelist.each_pair do |k, v|
+                v.each do |entry|
+                    if !member.has_key?(entry)
+                        member[entry] = {}
+                        member[entry].default = []
+                    end
+                    
+                    member[entry]["gene"] = [] if !member[entry].has_key?("gene")
+                    member[entry]["gene"].push(k)
+                end
+            end
+            
+            @length["gene"] = member.length
+            
+            complist.each_pair do |k, v|
+                v.each do |entry|
+                    if !member.has_key?(entry)
+                        member[entry] = {}
+                        member[entry].default = []
+                    end
+                    
+                    member[entry]["comp"] = [] if !member[entry].has_key?("comp")
+                    member[entry]["comp"].push(k)
+                end
+            end
+            
+            @length["comp"] = member.length - @length["gene"]
+            
+            return Sylfy::Feature.new(listnumber, member, length)
+            
+        end
+        #def enrichAnal(array, type = [])
+        #    featureCount = {}
+        #    array.each do |entry|
+        #        if featureMember.has_key?(entry[1])
+        #            
+        #        end
+        #        
+        #        featureMember[entry[0]]
+        #        featureCount[row[0]] = {} if !featureCount.has_key?(row[0])
+        #        featureCount[row[0]][row[1]] = 0 if !featureCount[row[0]].has_key?(row[1])
+        #    end
+        #    
+        #end
+    end
+    
+end
+
+