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 https://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 https://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 = <<EOF
PRAGMA page_size=4096;
PRAGMA main.locking_mode=EXCLUSIVE;

.separator '\t'

CREATE TABLE citations (
cit_id BIGINT,
cit_key VARCHAR(255),
pubmed_id BIGINT,
medline_id BIGINT,
ur LONGTEXT,
text LONGTEXT,
taxid_list LONGTEXT
);

CREATE TABLE delnodes (
tax_id BIGINT
);

CREATE TABLE division (
division_id     BIGINT,
division_cde VARCHAR(255),
division_name VARCHAR(255),
comments VARCHAR(255)
);

CREATE TABLE gencode (
genetic_code_id INT,
abbreviation VARCHAR(255),
name VARCHAR(255),
cde LONGTEXT,
starts LONGTEXT
);

CREATE TABLE merged (
old_tax_id BIGINT,
new_tax_id BIGINT
);

CREATE TABLE names (
tax_id BIGINT,
name_txt VARCHAR(255),
unique_name VARCHAR(255),
name_class VARCHAR(255)
);

CREATE TABLE nodes (
tax_id BIGINT,
parent_tax_id BIGINT,
rank VARCHAR(64),
embl_code VARCHAR(64),
division_id INTEGER,
inherited_div_flag BOOLEAN,
genetic_code_id INTEGER,
inherited_GC_flag BOOLEAN,
mitochondrial_genetic_code_id INTEGER,
inherited_MGC_flag BOOLEAN,
GenBank_hidden_flag BOOLEAN,
hidden_subtree_root_flag BOOLEAN,
comments VARCHAR(255)
);


CREATE INDEX citations_idx ON citations(cit_id,cit_key,pubmed_id,medline_id,ur,text,taxid_list);
CREATE INDEX delnodes_idx ON delnodes(tax_id);
CREATE INDEX division_idx ON division(division_id,division_cde,division_name,comments);
CREATE INDEX gencode_idx ON gencode(genetic_code_id,abbreviation,name,cde,starts);
CREATE INDEX merged_idx ON merged(old_tax_id,new_tax_id);
CREATE INDEX names_idx ON names(tax_id,name_txt,unique_name,name_class);
CREATE 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);


.import citations.dmp.trim citations
.import delnodes.dmp.trim delnodes
.import division.dmp.trim division
.import gencode.dmp.trim gencode
.import merged.dmp.trim merged
.import names.dmp.trim names
.import nodes.dmp.trim nodes

EOF
	`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