Class: Bio::DB::Primer3::SNP

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/db/primer3.rb

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize ⇒ SNP

Returns a new instance of SNP.



73
74
75
76
77
78
 
# File 'lib/bio/db/primer3.rb', line 73

def initialize
  @primers_line_1 = SortedSet.new
  @primers_line_2 = SortedSet.new
  @regions = SortedSet.new
  @primer3_errors = Set.new
end

Instance Attribute Details

#chromosome ⇒ Object

Returns the value of attribute chromosome.



58
59
60
 
# File 'lib/bio/db/primer3.rb', line 58

def chromosome
  @chromosome
end

#gene ⇒ Object

Returns the value of attribute gene.



58
59
60
 
# File 'lib/bio/db/primer3.rb', line 58

def gene
  @gene
end

#hit_count ⇒ Object

Returns the value of attribute hit_count.



66
67
68
 
# File 'lib/bio/db/primer3.rb', line 66

def hit_count
  @hit_count
end

#line_1 ⇒ Object

Returns the value of attribute line_1.



58
59
60
 
# File 'lib/bio/db/primer3.rb', line 58

def line_1
  @line_1
end

#line_2 ⇒ Object

Returns the value of attribute line_2.



58
59
60
 
# File 'lib/bio/db/primer3.rb', line 58

def line_2
  @line_2
end

#original ⇒ Object

Returns the value of attribute original.



58
59
60
 
# File 'lib/bio/db/primer3.rb', line 58

def original
  @original
end

#position ⇒ Object

Returns the value of attribute position.



58
59
60
 
# File 'lib/bio/db/primer3.rb', line 58

def position
  @position
end

#primer3_errors ⇒ Object

Returns the value of attribute primer3_errors.



64
65
66
 
# File 'lib/bio/db/primer3.rb', line 64

def primer3_errors
  @primer3_errors
end

#primer3_line_1 ⇒ Object

Returns the value of attribute primer3_line_1.



59
60
61
 
# File 'lib/bio/db/primer3.rb', line 59

def primer3_line_1
  @primer3_line_1
end

#primer3_line_2 ⇒ Object

Returns the value of attribute primer3_line_2.



59
60
61
 
# File 'lib/bio/db/primer3.rb', line 59

def primer3_line_2
  @primer3_line_2
end

#primers_line_1 ⇒ Object

Returns the value of attribute primers_line_1.



60
61
62
 
# File 'lib/bio/db/primer3.rb', line 60

def primers_line_1
  @primers_line_1
end

#primers_line_2 ⇒ Object

Returns the value of attribute primers_line_2.



60
61
62
 
# File 'lib/bio/db/primer3.rb', line 60

def primers_line_2
  @primers_line_2
end

#regions ⇒ Object

Returns the value of attribute regions.



63
64
65
 
# File 'lib/bio/db/primer3.rb', line 63

def regions
  @regions
end

#repetitive ⇒ Object

Returns the value of attribute repetitive.



65
66
67
 
# File 'lib/bio/db/primer3.rb', line 65

def repetitive
  @repetitive
end

#snp ⇒ Object

Returns the value of attribute snp.



58
59
60
 
# File 'lib/bio/db/primer3.rb', line 58

def snp
  @snp
end

#snp_from ⇒ Object

Returns the value of attribute snp_from.



62
63
64
 
# File 'lib/bio/db/primer3.rb', line 62

def snp_from
  @snp_from
end

#snp_type ⇒ Object

Returns the value of attribute snp_type.



67
68
69
 
# File 'lib/bio/db/primer3.rb', line 67

def snp_type
  @snp_type
end

#template_length ⇒ Object

Returns the value of attribute template_length.



59
60
61
 
# File 'lib/bio/db/primer3.rb', line 59

def template_length
  @template_length
end

#used_contigs ⇒ Object

Returns the value of attribute used_contigs.



61
62
63
 
# File 'lib/bio/db/primer3.rb', line 61

def used_contigs
  @used_contigs
end

Class Method Details

.parse(reg_str) ⇒ Object 



341
342
343
344
345
346
347
348
349
 
# File 'lib/bio/db/primer3.rb', line 341

def self.parse(reg_str)
  reg_str.chomp!
  snp = SNP.new
  snp.gene, snp.original, snp.position, snp.snp = reg_str.split(",")
  snp.position = snp.position.to_i
  snp.original.upcase!
  snp.snp.upcase!  
  snp
end

.parse_file(filename) ⇒ Object 



351
352
353
354
355
356
357
358
359
360
 
# File 'lib/bio/db/primer3.rb', line 351

def self.parse_file(filename)
  File.open(filename) do | f |
    f.each_line do | line |
      snp = SNP.parse(line)
      if snp.position > 0
        yield snp
      end
    end
  end
end

Instance Method Details

#add_record(primer3record) ⇒ Object 



363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
 
# File 'lib/bio/db/primer3.rb', line 363

def add_record(primer3record)
  @primer3_errors = Set.new unless @primer3_errors
  @template_length = primer3record.sequence_template.size
  if primer3record.primer_error != nil 
    primer3_errors << primer3record.primer_error
    return
  end
  case

  when primer3record.line == @line_1

    @line_1_template = primer3record.sequence_template

  when primer3record.line == @line_2
    @line_2_template = primer3record.sequence_template
  else
    raise Primer3Exception.new "#{primer3record.line} is not recognized (#{line_1}, #{line_2})"
  end

  if  primer3record.primer_left_num_returned.to_i > 0 
    case
    when primer3record.line == @line_1
      primers_line_1 << primer3record
      #puts primer3record.inspect
      @primer3_line_1 = primer3record if not @primer3_line_1  or @primer3_line_1 > primer3record
    when primer3record.line == @line_2
      primers_line_2 << primer3record
      @primer3_line_2 = primer3record if not @primer3_line_2  or @primer3_line_2 > primer3record
    else
      raise Primer3Exception.new "#{primer3record.line} is not recognized (#{line_1}, #{line_2})"
    end
  else
    primer3_errors << "#{primer3record.line}(#{primer3record.orientation}):#{primer3record.primer_left_explain.gsub!(',',';')}"
    primer3_errors << "common(#{primer3record.orientation}#{primer3record.type}):#{primer3record.primer_right_explain.gsub!(',',';')}"
    primer3_errors << "pair(#{primer3record.orientation}#{primer3record.type}):#{primer3record.primer_pair_explain.gsub!(',',';')}"
  end
end

#common_primer ⇒ Object 



272
273
274
275
 
# File 'lib/bio/db/primer3.rb', line 272

def common_primer 
  return self.values[9] if self.values[9] && self.values[9] != nil
  return ""
end

#find_left_primer_temp(primer) ⇒ Object 



88
89
90
91
92
93
94
95
96
 
# File 'lib/bio/db/primer3.rb', line 88

def find_left_primer_temp(primer)
  primers_line_1.each do |pr|
    return pr.find_left_tm(primer) if pr.find_left_tm(primer)
  end
  primers_line_2.each do |pr|
    return pr.find_left_tm(primer) if pr.find_left_tm(primer)
  end
  return "NA"
end

#find_primer_pair_first ⇒ Object 



99
100
101
102
103
104
105
 
# File 'lib/bio/db/primer3.rb', line 99

def find_primer_pair_first
  primers_line_1.each do |pr|
    primer = pr.left_primer_snp(self)
    return pr if find_left_primer_temp(primer) != "NA"
  end
  nil
end

#find_primer_pair_second ⇒ Object 



107
108
109
110
111
112
113
 
# File 'lib/bio/db/primer3.rb', line 107

def find_primer_pair_second
  primers_line_2.each do |pr|
    primer = pr.left_primer_snp(self)
    return pr if find_left_primer_temp(primer) != "NA"
  end
  nil
end

#first_primer ⇒ Object 



262
263
264
265
 
# File 'lib/bio/db/primer3.rb', line 262

def first_primer
  return self.values[7] if self.values[7] && self.values[7] != nil
  return ""
end

#first_product ⇒ Object 



288
289
290
291
292
293
294
295
296
297
298
 
# File 'lib/bio/db/primer3.rb', line 288

def first_product
  left = first_primer
  right = common_primer
  nlen = product_size - left.size - right.size
  product = left + ('n' * nlen) + Primer3Record.reverse_complement_string(right)
  #puts "orientation: #{orientation}"
  
  product = Primer3Record.reverse_complement_string(product)  if orientation == 'reverse'

  product
end

#found_primers? ⇒ Boolean

Returns:

  • (Boolean) 


258
259
260
 
# File 'lib/bio/db/primer3.rb', line 258

def found_primers?
  return self.values[7] && self.values[7] != nil
end

#line_1_name ⇒ Object 



69
70
71
 
# File 'lib/bio/db/primer3.rb', line 69

def line_1_name
  "#{gene}:#{position}#{original}>#{snp} #{line_1}}"
end

#line_2_name ⇒ Object 



80
81
82
 
# File 'lib/bio/db/primer3.rb', line 80

def line_2_name
  "#{gene}:#{position}#{original}>#{snp} #{line_2}}"
end

#orientation ⇒ Object 



282
283
284
285
 
# File 'lib/bio/db/primer3.rb', line 282

def orientation
  return self.values[11] if self.values[11]&& self.values[11] != nil 
  return 'unknown'
end

#print_primers ⇒ Object 



251
252
253
254
255
256
 
# File 'lib/bio/db/primer3.rb', line 251

def print_primers
  to_print = values.dup
  to_print << @repetitive
  to_print << @hit_count
  to_print.join(",")
end

#product_size ⇒ Object 



277
278
279
280
 
# File 'lib/bio/db/primer3.rb', line 277

def product_size
  return self.values[16].to_i if self.values[16]&& self.values[16] != nil 
  return 0
end

#realigned_primers ⇒ Object 



321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
 
# File 'lib/bio/db/primer3.rb', line 321

def realigned_primers
 
  return @realigned_primers if @realigned_primers
  sequences_to_align = Hash.new
  sequences_to_align["first_product"]  = first_product
  sequences_to_align["second_product"] = second_product
  sequences_to_align.merge!(snp_from.surrounding_exon_sequences)
  if sequences_to_align.size == 1
    @realigned_primers = sequences_to_align
    return @realigned_primers
  end
  options = ['--maxiterate', '1000', '--localpair', '--quiet']
  mafft = Bio::MAFFT.new( "mafft" , options)
  #puts "Before MAFT:#{sequences_to_align.inspect}"
  report = mafft.query_align(sequences_to_align)
  @realigned_primers = report.alignment
  #puts "MAFFT: #{report.alignment.inspect}" 
  @realigned_primers
end

#realigned_primers_fasta ⇒ Object 



312
313
314
315
316
317
318
 
# File 'lib/bio/db/primer3.rb', line 312

def realigned_primers_fasta
  ret_str = ""
  realigned_primers.each_pair do |name, seq|
    ret_str << ">#{self.to_s}-#{name}\n#{seq}\n" 
  end
  ret_str 
end

#second_primer ⇒ Object 



267
268
269
270
 
# File 'lib/bio/db/primer3.rb', line 267

def second_primer
  return self.values[8] if self.values[8] && self.values[8] != nil
  return ""
end

#second_product ⇒ Object 



300
301
302
303
304
305
306
307
308
309
 
# File 'lib/bio/db/primer3.rb', line 300

def second_product
  left = second_primer
  right = common_primer
  nlen = product_size - left.size - right.size
  product = left + ('n' * nlen) + Primer3Record.reverse_complement_string(right)
  product = Primer3Record.reverse_complement_string(product) if orientation == 'reverse'
  

  product
end

#to_s ⇒ Object 



84
85
86
 
# File 'lib/bio/db/primer3.rb', line 84

def to_s
  "#{gene}:#{original}#{position}#{snp}:#{snp_from.chromosome}"
end

#values ⇒ Object 



115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
 
# File 'lib/bio/db/primer3.rb', line 115

def values
  return @values if @values
  left_start = 0
  left_end = 0
  right_start = 0
  right_end = 0
  total_columns_before_messages=17
  #puts "Values in primer3"
  #puts snp_from.inspect
  @values = Array.new
  #@values << "#{gene},,#{template_length},"
  @values << gene
  @values << "#{original}#{position}#{snp}"
  @values << template_length
  @values << snp_from.chromosome
  @values << regions.size
  @values << regions.join("|")
  @values << snp_type
  if primer3_line_1 and primer3_line_2
    #Block that searches both if both pairs have a TM
    primer_1    = primer3_line_1.left_primer_with_coordinates(primer3_line_2.left_coordinates, primer3_line_2.orientation) 
    primer_1_tm = find_left_primer_temp(primer_1)

    primer_2    = primer3_line_2.left_primer_with_coordinates(primer3_line_1.left_coordinates, primer3_line_1.orientation)
    primer_2_tm = find_left_primer_temp(primer_2)

    if primer3_line_1 < primer3_line_2 and primer_2_tm != "NA"
      @values << primer3_line_1.left_primer
      @values << primer_2
      @values << primer3_line_1.right_primer 
      @values << primer3_line_1.type.to_s 
      @values << primer3_line_1.orientation.to_s 
      @values << primer3_line_1.best_pair.left.tm 
      @values << primer_2_tm
      @values << primer3_line_1.best_pair.right.tm
      @values << "first" 
      @values << primer3_line_1.best_pair.product_size
    elsif  primer_1_tm != "NA"
      @values << primer_1
      @values << primer3_line_2.left_primer
      @values << primer3_line_2.right_primer
      @values << primer3_line_2.type.to_s
      @values << primer3_line_2.orientation.to_s
      @values << primer_1_tm
      @values << primer3_line_2.best_pair.left.tm
      @values << primer3_line_2.best_pair.right.tm
      @values << "second"
      @values << primer3_line_2.best_pair.product_size
    else

      first_candidate  = find_primer_pair_first
      second_candidate = find_primer_pair_second

      if first_candidate
        primer_2 = primer3_line_2.left_primer_with_coordinates(first_candidate.left_coordinates, first_candidate.orientation)
        primer_2_tm = find_left_primer_temp(primer_2)
      end
      if second_candidate
        #puts "input to search #{first_candidate.left_coordinates}"
        primer_1 = primer3_line_1.left_primer_with_coordinates(second_candidate.left_coordinates, second_candidate.orientation) 
        primer_1_tm = find_left_primer_temp(primer_1)
        #puts "In the other funky if #{primer_2}"
      end

      if first_candidate and second_candidate and first_candidate < second_candidate 
        #puts "A"
        @values << first_candidate.left_primer
        @values << primer_2
        @values << first_candidate.right_primer 
        @values << first_candidate.type.to_s 
        @values << first_candidate.orientation.to_s 
        @values << first_candidate.best_pair.left.tm 
        @values << primer_2_tm
        @values << first_candidate.best_pair.right.tm
        @values << "first-" 
        @values << first_candidate.best_pair.product_size
      elsif  second_candidate 
        #puts "B"
        @values << primer_1
        @values << second_candidate.left_primer
        @values << second_candidate.right_primer
        @values << second_candidate.type.to_s
        @values << second_candidate.orientation.to_s
        @values << primer_1_tm
        @values << second_candidate.best_pair.left.tm
        @values << second_candidate.best_pair.right.tm
        @values << "second-"
        @values << second_candidate.best_pair.product_size
      elsif  first_candidate 
        #puts "C"
        @values << first_candidate.left_primer
        @values << primer_2
        @values << first_candidate.right_primer
        @values << first_candidate.type.to_s
        @values << first_candidate.orientation.to_s
        @values << primer_2_tm
        @values << first_candidate.best_pair.left.tm
        @values << first_candidate.best_pair.right.tm
        @values << "first/"
        @values << first_candidate.best_pair.product_size
      end
    end

  elsif primer3_line_1 
    @values << primer3_line_1.left_primer
    @values << primer3_line_1.left_primer_snp(self) 
    @values << primer3_line_1.right_primer 
    @values << primer3_line_1.type.to_s 
    @values << primer3_line_1.orientation.to_s      
    @values << primer3_line_1.best_pair.left.tm 
    @values << "NA"
    @values << primer3_line_1.best_pair.right.tm

    @values << "first+"
    @values << primer3_line_1.best_pair.product_size
  elsif primer3_line_2 
    @values << primer3_line_2.left_primer_snp(self) 
    @values << primer3_line_2.left_primer
    @values << primer3_line_2.right_primer
    @values << primer3_line_2.type.to_s
    @values << primer3_line_2.orientation.to_s
    @values << "NA"
    @values << primer3_line_2.best_pair.left.tm
    @values << primer3_line_2.best_pair.right.tm
    @values << "second+"
    @values << primer3_line_2.best_pair.product_size

  end 
  if @values.size < total_columns_before_messages
    @values[total_columns_before_messages] = primer3_errors.to_a.join("|")
  else
    @values << nil
  end
  return @values
end