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"
	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 37

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 62

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 80

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 135

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 99

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 141

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 147

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 48

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 68

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 74

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 56

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 52

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 42

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 29

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