Class: Taxonomy

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

Instance Method Summary collapse

Constructor Details

#initialize ⇒ Taxonomy

Returns a new instance of Taxonomy.



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# File 'lib/ncbi_taxonomy.rb', line 16

def initialize
  @home_dir = Dir.home
  @work_dir = @home_dir + "/.ncbi_taxonomy"
  @taxdb_release = @work_dir + "/taxonomy.db"
  @in_memory = false
  begin
    @db = SQLite3::Database.new @taxdb_release
  rescue SQLite3::CantOpenException => e
    STDERR.puts "Please download the NCBI Taxonomy database using 'ncbi_taxonomy update' command."
    STDERR.puts "[MSG]" + e.message
    exit 1
  end
end

Instance Method Details

#check_sqlite_version ⇒ Object 



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# File 'lib/ncbi_taxonomy.rb', line 43

def check_sqlite_version
  rs = @db.execute "SELECT SQLITE_VERSION()"
  Gem::Version.new(rs[0][0]) >= Gem::Version.new('3.8.3')
end

#get_all_names_by_id(id) ⇒ Object 



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# File 'lib/ncbi_taxonomy.rb', line 68

def get_all_names_by_id id
  id = id.to_i
  out = @db.execute "SELECT name_txt FROM names WHERE tax_id=#{id}"
  out
end

#get_allrank_by_id(id) ⇒ Object 



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# File 'lib/ncbi_taxonomy.rb', line 86

def get_allrank_by_id id
  id = id.to_i
  out = Array.new
  if check_sqlite_version
    rs = @db.execute "WITH RECURSIVE allrank (id, pid, rank, name) AS ( VALUES (0, #{id}, 'no_rank', 'Homo sapiens javamintus') UNION ALL SELECT nodes.tax_id, nodes.parent_tax_id, nodes.rank, names.name_txt FROM nodes, names, allrank WHERE nodes.tax_id=allrank.pid AND names.tax_id = nodes.tax_id AND names.name_class='scientific name' AND nodes.tax_id<>1) SELECT * FROM allrank;"
    rs[1..-2].each {|x| out << [ x[2], x[3] ] }
  else
    while true
      rs = self.get_rank_ptaxonid_scientificname_by_id id
      out << [ rs[1], rs[2] ]
      break if rs[1] == 'superkingdom'
      id = rs[0]
    end
  end

  out = self.get_allrank_by_id(self.get_missing_id id).reverse  if out.size == 0 && id > -1
  out.reverse
end

#get_allrank_by_name(name) ⇒ Object 



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# File 'lib/ncbi_taxonomy.rb', line 141

def get_allrank_by_name name
  out = Array.new
  self.get_taxonids_by_name(name).each {|x| out << self.get_allrank_by_id(x) }
  out
end

#get_fixedrank_by_id(id) ⇒ Object 



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# File 'lib/ncbi_taxonomy.rb', line 105

def get_fixedrank_by_id id
  id = id.to_i
  ranks = self.get_allrank_by_id id
  arr = Array.new
  pos = 0  
  alt_name = ''
  ranks.each do |rank, name|
    rank_fixed_no = tax_rank_fixed[rank]
    rank_all_no = tax_rank_all[rank]
    if rank_fixed_no != nil
      this_rank_fixed = tax_rank_fixed.to_a.index [rank, rank_fixed_no]
      if arr.size < this_rank_fixed
        (arr.size...this_rank_fixed).each do |x|
          arr << [ tax_rank_fixed.to_a[x][0], "@#{alt_name}_#{tax_rank_fixed.to_a[x][0]}" ]
          pos += 1
        end
      end
      arr << [ rank, name ]
      pos += 1
      alt_name = name
    elsif arr.size == 7 && rank_all_no == 28
      arr << [ 'strain', name ]
    elsif rank_all_no != 28
      alt_name = name if tax_rank_fixed.to_a[pos-1][1] > tax_rank_all[rank]
    end
  end
  if arr.size < 7 && arr.size >= 0
    (arr.size..7).each do |x|
      arr << [ tax_rank_fixed.to_a[x][0], nil ]
    end
  elsif arr.size == 7
    arr << [ 'strain', arr[-1][1] ]
  end
  arr
end

#get_fixedrank_by_name(name) ⇒ Object 



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# File 'lib/ncbi_taxonomy.rb', line 147

def get_fixedrank_by_name name
  out = Array.new
  self.get_taxonids_by_name(name).each {|x| out << self.get_fixedrank_by_id(x) }
  out
end

#get_missing_id(id) ⇒ Object 



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# File 'lib/ncbi_taxonomy.rb', line 153

def get_missing_id id
  rs = @db.execute "SELECT tax_id FROM delnodes WHERE tax_id='#{id}'"
  if rs.size > 0
    return -1
  else
    rs = @db.execute "SELECT new_tax_id FROM merged WHERE old_tax_id=#{id}"
    if rs.size == 1
      return rs[0][0].to_i
    else
      return -1
    end
  end
end

#get_names_by_taxonid(id) ⇒ Object 



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# File 'lib/ncbi_taxonomy.rb', line 54

def get_names_by_taxonid id
  @db.execute "SELECT name_class, name_txt FROM names WHERE tax_id=#{id}"
end

#get_rank_ptaxonid_by_id(id) ⇒ Object 



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# File 'lib/ncbi_taxonomy.rb', line 74

def get_rank_ptaxonid_by_id id
  id = id.to_i
  out = @db.execute "SELECT parent_tax_id, rank FROM nodes WHERE tax_id=#{id}"
  out[0]
end

#get_rank_ptaxonid_scientificname_by_id(id) ⇒ Object 



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# File 'lib/ncbi_taxonomy.rb', line 80

def get_rank_ptaxonid_scientificname_by_id id
  id = id.to_i
  out = @db.execute "SELECT nodes.parent_tax_id, nodes.rank, names.name_txt FROM nodes, names WHERE nodes.tax_id=#{id} AND names.tax_id=#{id} AND names.name_class='scientific name'"
  out[0]
end

#get_scientific_name_by_id(id) ⇒ Object 



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# File 'lib/ncbi_taxonomy.rb', line 62

def get_scientific_name_by_id id
  id = id.to_i
  out = @db.execute "SELECT name_txt FROM names WHERE tax_id=#{id} AND name_class='scientific name'"
  out[0][0]
end

#get_scientific_name_by_names(names) ⇒ Object 



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# File 'lib/ncbi_taxonomy.rb', line 58

def get_scientific_name_by_names names
  names.each {|x| return x[1] if x[0] == 'scientific name' }
end

#get_taxonids_by_name(name) ⇒ Object 



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# File 'lib/ncbi_taxonomy.rb', line 48

def get_taxonids_by_name name
  name = SQLite3::Database.quote name
  out = @db.execute "SELECT DISTINCT tax_id FROM names WHERE name_txt='#{name}'"
  out.flatten
end

#memory ⇒ Object 



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# File 'lib/ncbi_taxonomy.rb', line 30

def memory
  tmp = SQLite3::Database.new ':memory:'
  backup = SQLite3::Backup.new tmp, 'main', @db, 'main'
  backup.step -1
  backup.finish
  @db = tmp
  @in_memory = true
end

#memory? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/ncbi_taxonomy.rb', line 39

def memory?
  @in_memory
end

#tax_rank_all ⇒ Object 



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# File 'lib/ncbi_taxonomy.rb', line 12

def tax_rank_all
  { "superkingdom" => 0, "kingdom" => 1, "subkingdom" => 2, "superphylum" => 3, "phylum" => 4, "subphylum" => 5, "superclass" => 6, "class" => 7, "infraclass" => 8, "subclass" => 9, "superorder" => 10, "order" => 11, "suborder" => 12, "infraorder" => 13, "parvorder" => 14, "superfamily" => 15, "family" => 16, "subfamily" => 17, "tribe" => 18, "subtribe" => 19, "genus" => 20, "subgenus" => 21, "species group" => 22, "species subgroup" => 23, "species" => 24, "subspecies" => 25, "varietas" => 26, "forma" => 27, "no rank" => 28 }
end

#tax_rank_fixed ⇒ Object 



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# File 'lib/ncbi_taxonomy.rb', line 8

def tax_rank_fixed
  { "superkingdom" => 0, "phylum" => 4, "class" => 7, "order" => 11, "family" => 16, "genus" => 21, "species" => 24, "strain" => 28 }
end

#using_unique_name ⇒ Object 



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# File 'lib/ncbi_taxonomy.rb', line 4

def using_unique_name
  { "Ponticoccus" => 1, "Bacillus" => 1 }
end