class Bio::REBASE
bio/db/rebase.rb - Interface for EMBOSS formatted REBASE files
- Author
-
Trevor Wennblom <trevor@corevx.com>
- Copyright
-
Copyright © 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)
- License
-
The Ruby License
Description¶ ↑
Bio::REBASE provides utilties for interacting with REBASE data in EMBOSS format. REBASE is the Restriction Enzyme Database, more information can be found here:
EMBOSS formatted files located at:
These files are the same as the “emboss_?.???” files located at:
To easily get started with the data you can simply type this command at your shell prompt:
%Q wget "ftp://ftp.neb.com/pub/rebase/emboss_*"
Usage¶ ↑
require 'bio' require 'pp' enz = File.read('emboss_e') ref = File.read('emboss_r') sup = File.read('emboss_s') # When creating a new instance of Bio::REBASE # the contents of the enzyme file must be passed. # The references and suppiers file contents # may also be passed. rebase = Bio::REBASE.new( enz ) rebase = Bio::REBASE.new( enz, ref ) rebase = Bio::REBASE.new( enz, ref, sup ) # The 'read' class method allows you to read in files # that are REBASE EMBOSS formatted rebase = Bio::REBASE.read( 'emboss_e' ) rebase = Bio::REBASE.read( 'emboss_e', 'emboss_r' ) rebase = Bio::REBASE.read( 'emboss_e', 'emboss_r', 'emboss_s' ) # The data loaded may be saved in YAML format rebase.save_yaml( 'enz.yaml' ) rebase.save_yaml( 'enz.yaml', 'ref.yaml' ) rebase.save_yaml( 'enz.yaml', 'ref.yaml', 'sup.yaml' ) # YAML formatted files can also be read with the # class method 'load_yaml' rebase = Bio::REBASE.load_yaml( 'enz.yaml' ) rebase = Bio::REBASE.load_yaml( 'enz.yaml', 'ref.yaml' ) rebase = Bio::REBASE.load_yaml( 'enz.yaml', 'ref.yaml', 'sup.yaml' ) pp rebase.enzymes[0..4] # ["AarI", "AasI", "AatI", "AatII", "Acc16I"] pp rebase.enzyme_name?('aasi') # true pp rebase['AarI'].pattern # "CACCTGC" pp rebase['AarI'].blunt? # false pp rebase['AarI'].organism # "Arthrobacter aurescens SS2-322" pp rebase['AarI'].source # "A. Janulaitis" pp rebase['AarI'].primary_strand_cut1 # 11 pp rebase['AarI'].primary_strand_cut2 # 0 pp rebase['AarI'].complementary_strand_cut1 # 15 pp rebase['AarI'].complementary_strand_cut2 # 0 pp rebase['AarI'].suppliers # ["F"] pp rebase['AarI'].supplier_names # ["Fermentas International Inc."] pp rebase['AarI'].isoschizomers # Currently none stored in the references file pp rebase['AarI'].methylation # "" pp rebase['EcoRII'].methylation # "2(5)" pp rebase['EcoRII'].suppliers # ["F", "J", "M", "O", "S"] pp rebase['EcoRII'].supplier_names # ["Fermentas International Inc.", "Nippon Gene Co., Ltd.", # "Roche Applied Science", "Toyobo Biochemicals", # "Sigma Chemical Corporation"] # Number of enzymes in the database pp rebase.size # 673 pp rebase.enzymes.size # 673 rebase.each do |name, info| pp "#{name}: #{info.methylation}" unless info.methylation.empty? end
Public Class Methods
Read YAML formatted files
rebase = Bio::REBASE.load_yaml( 'enz.yaml' ) rebase = Bio::REBASE.load_yaml( 'enz.yaml', 'ref.yaml' ) rebase = Bio::REBASE.load_yaml( 'enz.yaml', 'ref.yaml', 'sup.yaml' )
Arguments
-
f_enzyme
: (required) Filename to read YAML-formatted enzyme data -
f_reference
: (optional) Filename to read YAML-formatted reference data -
f_supplier
: (optional) Filename to read YAML-formatted supplier data
- Returns
-
Bio::REBASE object
# File lib/bio/db/rebase.rb, line 258 def self.load_yaml( f_enzyme, f_reference=nil, f_supplier=nil ) e = YAML.load_file(f_enzyme) r = f_reference ? YAML.load_file(f_reference) : nil s = f_supplier ? YAML.load_file(f_supplier) : nil self.new(e,r,s,true) end
Constructor
Arguments
-
enzyme_lines
: (required) contents of EMBOSS formatted enzymes file -
reference_lines
: (optional) contents of EMBOSS formatted references file -
supplier_lines
: (optional) contents of EMBOSS formatted suppliers files -
yaml
: (optional, defaultfalse
) enzyme_lines, reference_lines, and supplier_lines are read as YAML if set to true
- Returns
# File lib/bio/db/rebase.rb, line 174 def initialize( enzyme_lines, reference_lines = nil, supplier_lines = nil, yaml = false ) # All your REBASE are belong to us. if yaml @enzyme_data = enzyme_lines @reference_data = reference_lines @supplier_data = supplier_lines else @enzyme_data = parse_enzymes(enzyme_lines) @reference_data = parse_references(reference_lines) @supplier_data = parse_suppliers(supplier_lines) end EnzymeEntry.supplier_data = @supplier_data setup_enzyme_data end
Read REBASE EMBOSS-formatted files
rebase = Bio::REBASE.read( 'emboss_e' ) rebase = Bio::REBASE.read( 'emboss_e', 'emboss_r' ) rebase = Bio::REBASE.read( 'emboss_e', 'emboss_r', 'emboss_s' )
Arguments
-
f_enzyme
: (required) Filename to read enzyme data -
f_reference
: (optional) Filename to read reference data -
f_supplier
: (optional) Filename to read supplier data
- Returns
-
Bio::REBASE object
# File lib/bio/db/rebase.rb, line 240 def self.read( f_enzyme, f_reference=nil, f_supplier=nil ) e = IO.readlines(f_enzyme) r = f_reference ? IO.readlines(f_reference) : nil s = f_supplier ? IO.readlines(f_supplier) : nil self.new(e,r,s) end
Public Instance Methods
Calls block once for each element in @data
hash,
passing that element as a parameter.
Arguments
-
Accepts a block
- Returns
-
results of block operations
# File lib/bio/db/rebase.rb, line 150 def each @data.each { |item| yield item } end
Check if supplied name is the name of an available enzyme
Arguments
-
name
: Enzyme name
- Returns
-
true/false
# File lib/bio/db/rebase.rb, line 207 def enzyme_name?(name) @enzyme_names_downcased.include?(name.downcase) end
List the enzymes available
Arguments
-
none
- Returns
-
Array
sorted enzyme names
# File lib/bio/db/rebase.rb, line 197 def enzymes @enzyme_names end
Save the current data
rebase.save_yaml( 'enz.yaml' ) rebase.save_yaml( 'enz.yaml', 'ref.yaml' ) rebase.save_yaml( 'enz.yaml', 'ref.yaml', 'sup.yaml' )
Arguments
-
f_enzyme
: (required) Filename to save YAML formatted output of enzyme data -
f_reference
: (optional) Filename to save YAML formatted output of reference data -
f_supplier
: (optional) Filename to save YAML formatted output of supplier data
- Returns
-
nothing
# File lib/bio/db/rebase.rb, line 222 def save_yaml( f_enzyme, f_reference=nil, f_supplier=nil ) File.open(f_enzyme, 'w') { |f| f.puts YAML.dump(@enzyme_data) } File.open(f_reference, 'w') { |f| f.puts YAML.dump(@reference_data) } if f_reference File.open(f_supplier, 'w') { |f| f.puts YAML.dump(@supplier_data) } if f_supplier return end
Protected Instance Methods
data is a hash indexed by the :name of each entry which is also a hash
-
data has the following keys: :name, :pattern, :len, :ncuts, :blunt, :c1, :c2, :c3, :c4 :c1 => First 5' cut :c2 => First 3' cut :c3 => Second 5' cut :c4 => Seocnd 3' cut
# File lib/bio/db/rebase.rb, line 314 def parse_enzymes( lines ) data = {} return data if lines == nil lines.each_line do |line| next if line[0].chr == '#' line.chomp! a = line.split("\s") data[ a[0] ] = { :name => a[0], :pattern => a[1], :len => a[2], :ncuts => a[3], :blunt => a[4], :c1 => a[5], :c2 => a[6], :c3 => a[7], :c4 => a[8] } end # lines.each data end
data is a hash indexed by the :name of each entry which is also a hash
-
data has the following keys: :organism, :isoschizomers, :references, :source, :methylation, :suppliers, :name, :number_of_references
# File lib/bio/db/rebase.rb, line 341 def parse_references( lines ) data = {} return data if lines == nil index = 1 h = {} references_left = 0 lines.each_line do |line| next if line[0].chr == '#' # Comment next if line[0..1] == '//' # End of entry marker line.chomp! if (1..7).include?( index ) h[index] = line references_left = h[index].to_i if index == 7 index += 1 next end if index == 8 h[index] ||= [] h[index] << line references_left -= 1 end if references_left == 0 data[ h[1] ] = { :name => h[1], :organism => h[2], :isoschizomers => h[3], :methylation => h[4], :source => h[5], :suppliers => h[6], :number_of_references => h[7], :references => h[8] } index = 1 h = {} end end # lines.each data end
data is a hash indexed by the supplier code
data[supplier_code] returns the suppliers name
# File lib/bio/db/rebase.rb, line 387 def parse_suppliers( lines ) data = {} return data if lines == nil lines.each_line do |line| next if line[0].chr == '#' data[$1] = $2 if line =~ %r{(.+?)\s(.+)} end data end
Takes a string in one of the three formats listed below and returns a Bio::Reference object
-
Possible input styles: a = 'Inagaki, K., Hikita, T., Yanagidani, S., Nomura, Y., Kishimoto, N., Tano, T., Tanaka, H., (1993) Biosci. Biotechnol. Biochem., vol. 57, pp. 1716-1721.' b = 'Nekrasiene, D., Lapcinskaja, S., Kiuduliene, L., Vitkute, J., Janulaitis, A., Unpublished observations.' c = “Grigaite, R., Maneliene, Z., Janulaitis, A., (2002) Nucleic Acids Res., vol. 30.”
# File lib/bio/db/rebase.rb, line 403 def raw_to_reference( line ) a = line.split(', ') if a[-1] == 'Unpublished observations.' title = a.pop.chop pages = volume = year = journal = '' else title = '' pages_or_volume = a.pop.chop if pages_or_volume =~ %r{pp\.\s} pages = pages_or_volume pages.gsub!('pp. ', '') volume = a.pop else pages = '' volume = pages_or_volume end volume.gsub!('vol. ', '') year_and_journal = a.pop year_and_journal =~ %r{\((\d+)\)\s(.+)} year = $1 journal = $2 end authors = [] last_name = nil a.each do |e| if last_name authors << "#{last_name}, #{e}" last_name = nil else last_name = e end end ref = { 'title' => title, 'pages' => pages, 'volume' => volume, 'year' => year, 'journal' => journal, 'authors' => authors, } Bio::Reference.new(ref) end
# File lib/bio/db/rebase.rb, line 295 def setup_enzyme_and_reference_association return unless @reference_data @reference_data.each do |name, hash| d = @data[name] [:organism, :isoschizomers, :methylation, :source].each { |k| d[k] = hash[k] } d.suppliers = hash[:suppliers].split('') d.references = [] hash[:references].each { |k| d.references << raw_to_reference(k) } end end
# File lib/bio/db/rebase.rb, line 269 def setup_enzyme_data @data = {} @enzyme_data.each do |name, hash| @data[name] = EnzymeEntry.new d = @data[name] d.pattern = hash[:pattern] # d.blunt?= is a syntax error d[:blunt?] = (hash[:blunt].to_i == 1 ? true : false) d.primary_strand_cut1 = hash[:c1].to_i d.complementary_strand_cut1 = hash[:c2].to_i d.primary_strand_cut2 = hash[:c3].to_i d.complementary_strand_cut2 = hash[:c4].to_i # Set up keys just in case there's no reference data supplied [:organism, :isoschizomers, :methylation, :source].each { |k| d[k] = '' } d.suppliers = [] d.references = [] end @enzyme_names = @data.keys.sort @enzyme_names_downcased = @enzyme_names.map{|a| a.downcase} setup_enzyme_and_reference_association end