ncbi-taxonomy 0.2.7 → 0.2.8

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: c29cb5552e8e97c991ece58aa8eb0eb413a28a6b
+  metadata.gz: ba922fa5117153ff37efbfdd32d00f1ebab44bdc
+  data.tar.gz: 44cc81dbc4364b4d28e4ef579d9a010bc2dbf6d7
 SHA512:
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+  data.tar.gz: a1ee97cf153a9f6c7d307b00342bea1e43aee3a268a0ac499592c42c88c0e2aa3e52bff8207c4dc821863fb4da147c2b34d74dc5bddddb69137315ff36ee00ce

data/bin/ncbi_taxonomy

@@ -4,7 +4,7 @@ require 'ncbi_taxonomy_update'
 
 def help msg
 	STDERR.puts msg
-	STDERR.puts "usage: #{$0.split("/")[-1]} <command> {-r} {-f} <args>"
+	STDERR.puts "usage: #{$0.split("/")[-1]} <command> {-i} {-r} {-f} <args>"
 	STDERR.puts
 	STDERR.puts "These commands are used for search."
 	STDERR.puts "    name      Search taxonomic names using organism name with all ranks"
@@ -25,6 +25,10 @@ def help msg
 	#STDERR.puts "              example using file) ncbi_taxonomy fid -f list.txt"
 	STDERR.puts
 	STDERR.puts "Common option for search command"
+	STDERR.puts "    -i        read multiple names or taxon ids from file"
+	STDERR.puts "              example) $ ncbi_taxonomy name -i names_list.txt"
+	STDERR.puts "              example) $ ncbi_taxonomy id -i taxon_id_list.txt"
+	STDERR.puts
 	STDERR.puts "    -r        show each rank name in the result (default is hiding rank name)"
 	STDERR.puts "              example) $ ncbi_taxonomy name -r \"Escherichia coli SE11\""
 	STDERR.puts
@@ -50,20 +54,28 @@ def help msg
 	exit 1
 end
 
+def read_list f
+	list = Array.new
+	IO.foreach(f) do |el|
+		list << el.chomp unless el.chomp == ''
+	end
+	
+	list
+end
+
 def search command, arg, opts
-	t = Taxonomy.new
 	out = nil
 	if command =~ /^na/
-		outs = t.get_allrank_by_name arg
+		outs = $t.get_allrank_by_name arg
 		STDERR.puts "[WARNING] name in multiple taxon" if outs.size > 1
 	elsif command =~ /^fn/
-		outs = t.get_fixedrank_by_name arg
+		outs = $t.get_fixedrank_by_name arg
 		STDERR.puts "[WARNING] name in multiple taxon" if outs.size > 1
 	elsif command =~ /^id/
-		outs = t.get_allrank_by_id arg.to_i
+		outs = $t.get_allrank_by_id arg.to_i
 		outs = [ outs ]
 	elsif command =~ /^fi/
-		outs = t.get_fixedrank_by_id arg.to_i
+		outs = $t.get_fixedrank_by_id arg.to_i
 		outs = [ outs ]
 	else
 		help "Incorrect command: #{command}"
@@ -114,6 +126,8 @@ when 'update'
 	ARGV.shift == '-f' ? flag = true  : flag = false
 	update flag
 else
+	$t = Taxonomy.new
+	
 	while ARGV.size > 0
 		arg = ARGV.shift
 		if arg =~ /^-/
@@ -124,6 +138,14 @@ else
 	end
 
 	args.each do |x|
-		search command, x, opts
+		if opts.index('-i') != nil
+			#$t.memory unless $t.memory?
+			list = read_list x
+			list.each do |el|
+				search command, el, opts
+			end
+		else
+			search command, x, opts
+		end
 	end
 end

data/lib/ncbi_taxonomy.rb

@@ -17,6 +17,7 @@ class Taxonomy
 		@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
@@ -32,6 +33,11 @@ class Taxonomy
 		backup.step -1
 		backup.finish
 		@db = tmp
+		@in_memory = true
+	end
+	
+	def memory?
+		@in_memory
 	end
 
 	def check_sqlite_version
@@ -81,7 +87,7 @@ class Taxonomy
 		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 = @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

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: ncbi-taxonomy
 version: !ruby/object:Gem::Version
-  version: 0.2.7
+  version: 0.2.8
 platform: ruby
 authors:
 - Seok-Won Kim
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-08-15 00:00:00.000000000 Z
+date: 2016-08-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: sqlite3