class Bio::AAindex2
Description¶ ↑
Parser class for AAindex2, Amino Acid Index Database.
Examples¶ ↑
# auto-detection of data format by using Bio::AAindex class aax2 = Bio::AAindex.auto("DAYM780301.aaindex2") # parse a file and get contents aax2 = Bio::AAindex2.new("DAYM780301.aaindex2") aax2.entry_id aax2.matrix aax2.matrix[2,2] aax2.matrix('R', 'A') aax2['R', 'A']
References¶ ↑
Public Class Methods
Source
# File lib/bio/db/aaindex.rb 286 def initialize(entry) 287 super(entry) 288 end
Calls superclass method
Bio::AAindex::new
Public Instance Methods
Source
# File lib/bio/db/aaindex.rb 311 def [](aa1 = nil, aa2 = nil) 312 matrix[cols.index(aa1), rows.index(aa2)] 313 end
Returns the value of amino acids substitution (aa1 -> aa2).
Source
# File lib/bio/db/aaindex.rb 301 def cols 302 if @data['cols'] 303 @data['cols'] 304 else 305 label_data 306 @cols 307 end 308 end
Returns col labels.
Source
# File lib/bio/db/aaindex.rb 316 def matrix(aa1 = nil, aa2 = nil) 317 return self[aa1, aa2] if aa1 and aa2 318 319 if @data['matrix'] 320 @data['matrix'] 321 else 322 ma = [] 323 label_data.each_line do |line| 324 ma << line.strip.split(/\s+/).map {|x| x.to_f } 325 end 326 ma_len = ma.size 327 ma.each do |row| 328 row_size = row.size 329 if row_size < ma_len 330 (row_size..ma_len-1).each do |i| 331 row[i] = ma[i][row_size-1] 332 end 333 end 334 end 335 mat = Matrix[*ma] 336 @data['matrix'] = mat 337 end 338 end
Returns amino acids matrix in Matrix.
Source
# File lib/bio/db/aaindex.rb 341 def old_matrix # for AAindex <= ver 5.0 342 return @data['matrix'] if @data['matrix'] 343 344 @aa = {} 345 # used to determine row/column of the aa 346 attr_reader :aa 347 alias_method :aa, :rows 348 alias_method :aa, :cols 349 350 field = field_fetch('I') 351 352 case field 353 when / (ARNDCQEGHILKMFPSTWYV)\s+(.*)/ # 20x19/2 matrix 354 aalist = $1 355 values = $2.split(/\s+/) 356 357 0.upto(aalist.length - 1) do |i| 358 @aa[aalist[i].chr] = i 359 end 360 361 ma = Array.new 362 20.times do 363 ma.push(Array.new(20)) # 2D array of 20x(20) 364 end 365 366 for i in 0 .. 19 do 367 for j in i .. 19 do 368 ma[i][j] = values[i + j*(j+1)/2].to_f 369 ma[j][i] = ma[i][j] 370 end 371 end 372 @data['matrix'] = Matrix[*ma] 373 when / -ARNDCQEGHILKMFPSTWYV / # 21x20/2 matrix (with gap) 374 raise NotImplementedError 375 when / ACDEFGHIKLMNPQRSTVWYJ- / # 21x21 matrix (with gap) 376 raise NotImplementedError 377 end 378 end
Returns amino acids matrix in Matrix for the old format (<= ver 5.0).
Source
# File lib/bio/db/aaindex.rb 291 def rows 292 if @data['rows'] 293 @data['rows'] 294 else 295 label_data 296 @rows 297 end 298 end
Returns row labels.