Module: CASCADE

Extended by:
Resource
Defined in:
lib/rbbt/sources/CASCADE.rb

Constant Summary collapse

URL = 
'https://bitbucket.org/asmundf/cascade'

Class Method Summary collapse

Class Method Details

.process_interactions(file) ⇒ Object

self.search_paths = {} self.search_paths = :lib



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# File 'lib/rbbt/sources/CASCADE.rb', line 15

def self.process_interactions(file)
  io = Open.open(file)
  tsv = TSV.open(io, :merge => true, :header_hash => '')

  new_fields = ["ENTITYB"] + (tsv.fields - ["ENTITYB"])
  tsv = tsv.reorder :key, new_fields

  tsv.key_field = "ENTITYA (Associated Gene Name)"
  tsv.rename_field "ENTITYB", "ENTITYB (Associated Gene Name)"

  tsv.process "PMID" do |values|
    values.collect{|v| v.scan(/\d+/) * ";;"}
  end

  tsv
end

.process_members(file) ⇒ Object 



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# File 'lib/rbbt/sources/CASCADE.rb', line 32

def self.process_members(file)
  TSV.open(file, :merge => true, :header_hash => '', :type => :flat, :sep2 => /[,.]\s*/)
end

.process_paradigm(interactions, members) ⇒ Object 



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# File 'lib/rbbt/sources/CASCADE.rb', line 36

def self.process_paradigm(interactions, members)
  proteins = Set.new members.values.flatten.uniq
  outputs = Set.new
  associations = {}

  interactions.through do |source, values|
    values.zip_fields.each do |target,typea,ida,databasea,typeb,idb,databaseb,effect|
      next if typea == 'gene'

      if typeb == 'gene'
        target.sub!('_g','')
        type = '-t'
      elsif typeb == 'output' or typea == 'output'
        type = '-ap'
      else
        type = '-a'
      end

      proteins << source unless source.include? '_f' or source.include? '_c'
      proteins << target unless target.include? '_f' or target.include? '_c'

      outputs << source if typea == 'output'
      outputs << target if typeb == 'output'

      effect_symbol = '>' 
      effect_symbol = '|' if effect.include? 'inhibit'

      associations[[source,target]] = [type, effect_symbol]
    end
  end

  str = StringIO.new

  proteins.each do |p|
    next if outputs.include? p
    str.puts ["protein", p] * "\t"
  end

  outputs.each do |o|
    str.puts ["abstract", o] * "\t"
  end

  members.each do |e, targets|
    e = e.dup
    case 
    when e.include?('_c')
      str.puts ["complex", e] * "\t"
      type = 'component'
    when e.include?('_f')
      str.puts ["family", e] * "\t"
      type = 'member'
    else
      next
    end

    targets.each do |target|
      associations[[target,e]] = [type, '>']
    end
  end


  associations.each do |p,i|
    source, target = p
    type, symbol = i

    str.puts [source, target, [type,symbol]*""] * "\t"
  end

  str.rewind
  str
end