Class | Bio::REBASE |
In: |
lib/bio/db/rebase.rb
|
Parent: | Object |
bio/db/rebase.rb - Interface for EMBOSS formatted REBASE files
Author: | Trevor Wennblom <trevor@corevx.com> |
Copyright: | Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com) |
License: | The Ruby License |
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:
% wget ftp://ftp.neb.com/pub/rebase/emboss*
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
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
Returns: | Bio::REBASE object |
# File lib/bio/db/rebase.rb, line 261 261: def self.load_yaml( f_enzyme, f_reference=nil, f_supplier=nil ) 262: e = YAML.load_file(f_enzyme) 263: r = f_reference ? YAML.load_file(f_reference) : nil 264: s = f_supplier ? YAML.load_file(f_supplier) : nil 265: self.new(e,r,s,true) 266: end
Constructor
Arguments
Returns: | Bio::REBASE |
# File lib/bio/db/rebase.rb, line 174 174: def initialize( enzyme_lines, reference_lines = nil, supplier_lines = nil, yaml = false ) 175: # All your REBASE are belong to us. 176: 177: if yaml 178: @enzyme_data = enzyme_lines 179: @reference_data = reference_lines 180: @supplier_data = supplier_lines 181: else 182: @enzyme_data = parse_enzymes(enzyme_lines) 183: @reference_data = parse_references(reference_lines) 184: @supplier_data = parse_suppliers(supplier_lines) 185: end 186: 187: EnzymeEntry.supplier_data = @supplier_data 188: setup_enzyme_data 189: 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
Returns: | Bio::REBASE object |
# File lib/bio/db/rebase.rb, line 243 243: def self.read( f_enzyme, f_reference=nil, f_supplier=nil ) 244: e = IO.readlines(f_enzyme) 245: r = f_reference ? IO.readlines(f_reference) : nil 246: s = f_supplier ? IO.readlines(f_supplier) : nil 247: self.new(e,r,s) 248: end
Check if supplied name is the name of an available enzyme
Arguments
Returns: | +true/false+ |
# File lib/bio/db/rebase.rb, line 207 207: def enzyme_name?(name) 208: enzymes.each do |e| 209: return true if e.downcase == name.downcase 210: end 211: return false 212: 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
Returns: | nothing |
# File lib/bio/db/rebase.rb, line 225 225: def save_yaml( f_enzyme, f_reference=nil, f_supplier=nil ) 226: File.open(f_enzyme, 'w') { |f| f.puts YAML.dump(@enzyme_data) } 227: File.open(f_reference, 'w') { |f| f.puts YAML.dump(@reference_data) } if f_reference 228: File.open(f_supplier, 'w') { |f| f.puts YAML.dump(@supplier_data) } if f_supplier 229: return 230: end
data is a hash indexed by the :name of each entry which is also a hash
# File lib/bio/db/rebase.rb, line 315 315: def parse_enzymes( lines ) 316: data = {} 317: return data if lines == nil 318: lines.each_line do |line| 319: next if line[0].chr == '#' 320: line.chomp! 321: 322: a = line.split("\s") 323: 324: data[ a[0] ] = { 325: :name => a[0], 326: :pattern => a[1], 327: :len => a[2], 328: :ncuts => a[3], 329: :blunt => a[4], 330: :c1 => a[5], 331: :c2 => a[6], 332: :c3 => a[7], 333: :c4 => a[8] 334: } 335: end # lines.each 336: data 337: end
data is a hash indexed by the :name of each entry which is also a hash
# File lib/bio/db/rebase.rb, line 342 342: def parse_references( lines ) 343: data = {} 344: return data if lines == nil 345: index = 1 346: h = {} 347: references_left = 0 348: 349: lines.each_line do |line| 350: next if line[0].chr == '#' # Comment 351: next if line[0..1] == '//' # End of entry marker 352: line.chomp! 353: 354: if (1..7).include?( index ) 355: h[index] = line 356: references_left = h[index].to_i if index == 7 357: index += 1 358: next 359: end 360: 361: if index == 8 362: h[index] ||= [] 363: h[index] << line 364: references_left -= 1 365: end 366: 367: if references_left == 0 368: data[ h[1] ] = { 369: :name => h[1], 370: :organism => h[2], 371: :isoschizomers => h[3], 372: :methylation => h[4], 373: :source => h[5], 374: :suppliers => h[6], 375: :number_of_references => h[7], 376: :references => h[8] 377: } 378: index = 1 379: h = {} 380: end 381: end # lines.each 382: data 383: end
data is a hash indexed by the supplier code
data[supplier_code] returns the suppliers name
# File lib/bio/db/rebase.rb, line 388 388: def parse_suppliers( lines ) 389: data = {} 390: return data if lines == nil 391: lines.each_line do |line| 392: next if line[0].chr == '#' 393: data[$1] = $2 if line =~ %r{(.+?)\s(.+)} 394: end 395: data 396: end
Takes a string in one of the three formats listed below and returns a Bio::Reference object
# File lib/bio/db/rebase.rb, line 404 404: def raw_to_reference( line ) 405: a = line.split(', ') 406: 407: if a[-1] == 'Unpublished observations.' 408: title = a.pop.chop 409: pages = volume = year = journal = '' 410: else 411: title = '' 412: 413: pages_or_volume = a.pop.chop 414: if pages_or_volume =~ %r{pp\.\s} 415: pages = pages_or_volume 416: pages.gsub!('pp. ', '') 417: volume = a.pop 418: else 419: pages = '' 420: volume = pages_or_volume 421: end 422: 423: volume.gsub!('vol. ', '') 424: 425: year_and_journal = a.pop 426: year_and_journal =~ %r{\((\d+)\)\s(.+)} 427: year = $1 428: journal = $2 429: end 430: 431: authors = [] 432: 433: last_name = nil 434: a.each do |e| 435: if last_name 436: authors << "#{last_name}, #{e}" 437: last_name = nil 438: else 439: last_name = e 440: end 441: end 442: 443: ref = { 444: 'title' => title, 445: 'pages' => pages, 446: 'volume' => volume, 447: 'year' => year, 448: 'journal' => journal, 449: 'authors' => authors, 450: } 451: 452: Bio::Reference.new(ref) 453: end
# File lib/bio/db/rebase.rb, line 296 296: def setup_enzyme_and_reference_association 297: return unless @reference_data 298: @reference_data.each do |name, hash| 299: d = @data[name] 300: [:organism, :isoschizomers, 301: :methylation, :source].each { |k| d[k] = hash[k] } 302: d.suppliers = hash[:suppliers].split('') 303: d.references = [] 304: hash[:references].each { |k| d.references << raw_to_reference(k) } 305: end 306: end
# File lib/bio/db/rebase.rb, line 272 272: def setup_enzyme_data 273: @data = {} 274: 275: @enzyme_data.each do |name, hash| 276: @data[name] = EnzymeEntry.new 277: d = @data[name] 278: d.pattern = hash[:pattern] 279: # d.blunt?= is a syntax error 280: d[:blunt?] = (hash[:blunt].to_i == 1 ? true : false) 281: d.primary_strand_cut1 = hash[:c1].to_i 282: d.complementary_strand_cut1 = hash[:c2].to_i 283: d.primary_strand_cut2 = hash[:c3].to_i 284: d.complementary_strand_cut2 = hash[:c4].to_i 285: 286: # Set up keys just in case there's no reference data supplied 287: [:organism, :isoschizomers, 288: :methylation, :source].each { |k| d[k] = '' } 289: d.suppliers = [] 290: d.references = [] 291: end 292: 293: setup_enzyme_and_reference_association 294: end