Class: Update

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

Overview

Later, I should fix this.

Instance Method Summary collapse

Constructor Details

#initialize ⇒ Update

Returns a new instance of Update.



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# File 'lib/ncbi_taxonomy_update.rb', line 9

def initialize
  @home_dir = Dir.home
  @work_dir = @home_dir + "/.ncbi_taxonomy"
  md5_file = @work_dir + "/taxdump.tar.gz.md5"
  md5_old_file = @work_dir + "/taxdump.tar.gz.md5.old"
  @taxdb = @work_dir + "/taxonomy.db.prep"
  @taxdb_release = @work_dir + "/taxonomy.db"
  @status = nil

  # check workinng directory, if not exist, make it.
  if File.exist?(@work_dir)
    if !File.directory?(@work_dir)
      @status = "This software uses $HOME/.ncbi_taxonomy directory. However, in your home directory there is same name of file. We recommend you change that file name to another name."
      return
    else
      Dir.chdir @work_dir
      if File.exist?(md5_file)
        `rm -f #{md5_old_file}`
        File.rename(md5_file, md5_old_file)
        self.download_md5
        `diff #{md5_file} #{md5_old_file}`
        if $?.exitstatus == 0
          @status = false
          return
        else
          @status = true
          return
        end
      else
        self.download_md5
      end
    end
  else
    Dir.mkdir @work_dir
    Dir.chdir @work_dir
    self.download_md5
  end

  @status = true
  return
end

Instance Method Details

#do ⇒ Object 



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# File 'lib/ncbi_taxonomy_update.rb', line 87

def do
  self.download_dump
  self.substitution
  self.load_db
  self.release
end

#download_dump ⇒ Object 



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# File 'lib/ncbi_taxonomy_update.rb', line 59

def download_dump
  `curl -s ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz 2>/dev/null | tar zxf - `
end

#download_md5 ⇒ Object 



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# File 'lib/ncbi_taxonomy_update.rb', line 55

def download_md5
  `curl -s ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz.md5 > taxdump.tar.gz.md5 2>/dev/null`
end

#load_db ⇒ Object 



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# File 'lib/ncbi_taxonomy_update.rb', line 94

def load_db
  sql = "PRAGMA page_size=4096;\nPRAGMA main.locking_mode=EXCLUSIVE;\n\n.separator '\\t'\n\nCREATE TABLE citations (\ncit_id BIGINT,\ncit_key VARCHAR(255),\npubmed_id BIGINT,\nmedline_id BIGINT,\nur LONGTEXT,\ntext LONGTEXT,\ntaxid_list LONGTEXT\n);\n\nCREATE TABLE delnodes (\ntax_id BIGINT\n);\n\nCREATE TABLE division (\ndivision_id     BIGINT,\ndivision_cde VARCHAR(255),\ndivision_name VARCHAR(255),\ncomments VARCHAR(255)\n);\n\nCREATE TABLE gencode (\ngenetic_code_id INT,\nabbreviation VARCHAR(255),\nname VARCHAR(255),\ncde LONGTEXT,\nstarts LONGTEXT\n);\n\nCREATE TABLE merged (\nold_tax_id BIGINT,\nnew_tax_id BIGINT\n);\n\nCREATE TABLE names (\ntax_id BIGINT,\nname_txt VARCHAR(255),\nunique_name VARCHAR(255),\nname_class VARCHAR(255)\n);\n\nCREATE TABLE nodes (\ntax_id BIGINT,\nparent_tax_id BIGINT,\nrank VARCHAR(64), \nembl_code VARCHAR(64),\ndivision_id INTEGER,\ninherited_div_flag BOOLEAN,\ngenetic_code_id INTEGER,\ninherited_GC_flag BOOLEAN,\nmitochondrial_genetic_code_id INTEGER,\ninherited_MGC_flag BOOLEAN,\nGenBank_hidden_flag BOOLEAN,\nhidden_subtree_root_flag BOOLEAN,\ncomments VARCHAR(255)\n);\n\n\nCREATE INDEX citations_idx ON citations(cit_id,cit_key,pubmed_id,medline_id,ur,text,taxid_list);\nCREATE INDEX delnodes_idx ON delnodes(tax_id);\nCREATE INDEX division_idx ON division(division_id,division_cde,division_name,comments);\nCREATE INDEX gencode_idx ON gencode(genetic_code_id,abbreviation,name,cde,starts);\nCREATE INDEX merged_idx ON merged(old_tax_id,new_tax_id);\nCREATE INDEX names_idx ON names(tax_id,name_txt,unique_name,name_class);\nCREATE INDEX nodes_idx ON nodes(tax_id,parent_tax_id,rank,embl_code,division_id,inherited_div_flag,genetic_code_id,inherited_GC_flag,mitochondrial_genetic_code_id,inherited_MGC_flag,GenBank_hidden_flag,hidden_subtree_root_flag,comments);\n\n\n.import citations.dmp.trim citations\n.import delnodes.dmp.trim delnodes\n.import division.dmp.trim division\n.import gencode.dmp.trim gencode\n.import merged.dmp.trim merged\n.import names.dmp.trim names\n.import nodes.dmp.trim nodes\n  \n"
  `echo "#{sql}" | sqlite3 #{@taxdb} < /dev/stdin`
end

#release ⇒ Object 



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# File 'lib/ncbi_taxonomy_update.rb', line 75

def release
  begin
    FileUtils.rm "#{@taxdb_release}.old"
  rescue Errno::ENOENT => e
  end
  begin
    File.rename(@taxdb_release, @taxdb_release+".old")
  rescue Errno::ENOENT => e
  end
  File.rename(@taxdb, @taxdb_release)
end

#status ⇒ Object 



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# File 'lib/ncbi_taxonomy_update.rb', line 51

def status
  return @status
end

#substitution ⇒ Object

substitute some characters



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# File 'lib/ncbi_taxonomy_update.rb', line 64

def substitution
  Dir.entries(@work_dir).each do |file|
    if file =~ /dmp$/
      #STDERR.puts "treating #{file}"
      File.open(@work_dir+"/"+file+".trim","w") do |out|
        out << File.open(@work_dir+"/"+file).read.force_encoding('iso-8859-1').encode('utf-8').gsub(/([^|]) ([^|])/,'\1 \2').gsub(/\t\|\t/,"\t").gsub(/\t\|$/,"").gsub(/\"/,"%22")
      end
    end
  end
end