Class: Sylfy::Feature

Inherits:
Object
  • Object
show all
Defined in:
lib/sylfy/feature.rb

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Attribute Details

#length ⇒ Object (readonly)

Returns the value of attribute length.



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# File 'lib/sylfy/feature.rb', line 15

def length
  @length
end

#listnumber ⇒ Object (readonly)

Returns the value of attribute listnumber.



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# File 'lib/sylfy/feature.rb', line 15

def listnumber
  @listnumber
end

#member ⇒ Object (readonly)

Returns the value of attribute member.



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# File 'lib/sylfy/feature.rb', line 15

def member
  @member
end

Class Method Details

.fromKEGG(species = 'ref') ⇒ Object 



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# File 'lib/sylfy/feature.rb', line 53

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

.open(filename, options) ⇒ Object 



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# File 'lib/sylfy/feature.rb', line 25

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