Module: GNormPlus

Defined in:
lib/rbbt/ner/g_norm_plus.rb

Constant Summary collapse

CONFIG = 
<<-EOF

#===Annotation
#Attribution setting:
#FocusSpecies = Taxonomy ID
#	All: All species
#	9606: Human
#	4932: yeast
#	7227: Fly
#	10090: Mouse
#	10116: Rat
#	7955: Zebrafish
#	3702: Arabidopsis thaliana
#open: True
#close: False

[Focus Species]
	FocusSpecies = All
[Dictionary & Model]
	DictionaryFolder = ./Dictionary
	GNRModel = ./Dictionary/GNR.Model
	SCModel = ./Dictionary/SimConcept.Model
	GeneIDMatch = True
	Normalization2Protein = False
	DeleteTmp = True
EOF

Class Method Summary collapse

Class Method Details

.process(texts) ⇒ Object 



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# File 'lib/rbbt/ner/g_norm_plus.rb', line 39

def self.process(texts)
  TmpFile.with_file do |tmpdir|
    Open.mkdir tmpdir
    Misc.in_dir tmpdir do
      Open.ln_s Rbbt.software.opt.GNormPlus.Dictionary.find, '.'
      Open.ln_s Rbbt.software.opt.GNormPlus["BioC.dtd"].find, '.'
      Open.ln_s Rbbt.software.opt.GNormPlus["Ab3P"].find, '.'
      Open.ln_s Rbbt.software.opt.GNormPlus["CRF"].find, '.'
      Open.mkdir 'input'
      Open.mkdir 'output'
      Open.mkdir 'tmp'

      texts.each do |name,text|
        Open.write("input/#{name}.txt") do |f|
          f.puts "#{name}|a|" << text
          f.puts
        end
      end
      Open.write('config', CONFIG)
      CMD.cmd_log("java -Xmx20G -Xms20G  -jar '#{Rbbt.software.opt.GNormPlus.find}/GNormPlus.jar' 'input' 'output' 'config'")

      if texts.respond_to? :key_field
        key_field = texts.key_field
      else
        key_field = "ID"
      end
      tsv = TSV.setup({}, :key_field => key_field, :fields => ["Entities"], :type => :flat)
      Dir.glob("output/*.txt").each do |file|
        name = File.basename(file).sub(".txt",'')
        entities = Open.read(file).split("\n")[1..-1].collect{|l| l.gsub(':', '.').split("\t")[1..-1] * ":"}
        tsv[name] = entities
      end
      tsv
    end
  end
end