Class: Bio::Fasta::Report::Hit

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/appl/fasta/format10.rb

Defined Under Namespace

Classes: Query, Target

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(data) ⇒ Hit

Returns a new instance of Hit.



201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
 
# File 'lib/bio/appl/fasta/format10.rb', line 201

def initialize(data)
  score, query, target = data.split(/\n>/)

  @definition, *score = score.split(/\n/)
  @score = {}

  pat = /;\s+([^:]+):\s+(.*)/

  score.each do |x|
    if pat.match(x)
      @score[$1] = $2
    end
  end

  @query = Query.new(query)
  @target = Target.new(target)
end

Instance Attribute Details

#definition ⇒ Object (readonly)

Returns the value of attribute definition.



218
219
220
 
# File 'lib/bio/appl/fasta/format10.rb', line 218

def definition
  @definition
end

#query ⇒ Object (readonly)

Returns the value of attribute query.



218
219
220
 
# File 'lib/bio/appl/fasta/format10.rb', line 218

def query
  @query
end

#score ⇒ Object (readonly)

Returns the value of attribute score.



218
219
220
 
# File 'lib/bio/appl/fasta/format10.rb', line 218

def score
  @score
end

#target ⇒ Object (readonly)

Returns the value of attribute target.



218
219
220
 
# File 'lib/bio/appl/fasta/format10.rb', line 218

def target
  @target
end

Instance Method Details

#bit_score ⇒ Object

Bit score



234
235
236
237
238
239
240
241
242
243
244
 
# File 'lib/bio/appl/fasta/format10.rb', line 234

def bit_score
  if @score['fa_bits']
    @score['fa_bits'].to_f
  elsif @score['sw_bits']
    @score['sw_bits'].to_f
  elsif @score['fx_bits']
    @score['fx_bits'].to_f
  elsif @score['tx_bits']
    @score['tx_bits'].to_f
  end
end

#direction ⇒ Object 



246
247
248
 
# File 'lib/bio/appl/fasta/format10.rb', line 246

def direction
  @score['fa_frame'] || @score['sw_frame'] || @score['fx_frame'] || @score['tx_frame']
end

#evalue ⇒ Object

E-value score



221
222
223
224
225
226
227
228
229
230
231
 
# File 'lib/bio/appl/fasta/format10.rb', line 221

def evalue
  if @score['fa_expect']
    @score['fa_expect'].to_f
  elsif @score['sw_expect']
    @score['sw_expect'].to_f
  elsif @score['fx_expect']
    @score['fx_expect'].to_f
  elsif @score['tx_expect']
    @score['tx_expect'].to_f
  end
end

#identity ⇒ Object

percent identity



256
257
258
 
# File 'lib/bio/appl/fasta/format10.rb', line 256

def identity
  @score['sw_ident'].to_f
end

#lap_at ⇒ Object 



327
328
329
 
# File 'lib/bio/appl/fasta/format10.rb', line 327

def lap_at
  [ query_start, query_end, target_start, target_end ]
end

#overlap ⇒ Object

overlap length



261
262
263
 
# File 'lib/bio/appl/fasta/format10.rb', line 261

def overlap
  @score['sw_overlap'].to_i
end

#query_def ⇒ Object 



275
276
277
 
# File 'lib/bio/appl/fasta/format10.rb', line 275

def query_def
  @query.definition
end

#query_end ⇒ Object 



315
316
317
 
# File 'lib/bio/appl/fasta/format10.rb', line 315

def query_end
  @query.stop
end

#query_id ⇒ Object

Shortcuts for the methods of Bio::Fasta::Report::Hit::Query



267
268
269
 
# File 'lib/bio/appl/fasta/format10.rb', line 267

def query_id
  @query.entry_id
end

#query_len ⇒ Object 



283
284
285
 
# File 'lib/bio/appl/fasta/format10.rb', line 283

def query_len
  @query.length
end

#query_seq ⇒ Object 



293
294
295
 
# File 'lib/bio/appl/fasta/format10.rb', line 293

def query_seq
  @query.sequence
end

#query_start ⇒ Object

Information on matching region



311
312
313
 
# File 'lib/bio/appl/fasta/format10.rb', line 311

def query_start
  @query.start
end

#query_type ⇒ Object 



301
302
303
 
# File 'lib/bio/appl/fasta/format10.rb', line 301

def query_type
  @query.moltype
end

#sw ⇒ Object

Smith-Waterman score



251
252
253
 
# File 'lib/bio/appl/fasta/format10.rb', line 251

def sw
  @score['sw_score'].to_i
end

#target_def ⇒ Object 



279
280
281
 
# File 'lib/bio/appl/fasta/format10.rb', line 279

def target_def
  @target.definition
end

#target_end ⇒ Object 



323
324
325
 
# File 'lib/bio/appl/fasta/format10.rb', line 323

def target_end
  @target.stop
end

#target_id ⇒ Object 



271
272
273
 
# File 'lib/bio/appl/fasta/format10.rb', line 271

def target_id
  @target.entry_id
end

#target_len ⇒ Object

Shortcuts for the methods of Bio::Fasta::Report::Hit::Target



289
290
291
 
# File 'lib/bio/appl/fasta/format10.rb', line 289

def target_len
  @target.length
end

#target_seq ⇒ Object 



297
298
299
 
# File 'lib/bio/appl/fasta/format10.rb', line 297

def target_seq
  @target.sequence
end

#target_start ⇒ Object 



319
320
321
 
# File 'lib/bio/appl/fasta/format10.rb', line 319

def target_start
  @target.start
end

#target_type ⇒ Object 



305
306
307
 
# File 'lib/bio/appl/fasta/format10.rb', line 305

def target_type
  @target.moltype
end