Class: TestCode

Inherits:
Object
  • Object
show all
Defined in:
lib/full_lengther_next/classes/test_code.rb

Instance Method Summary collapse

Constructor Details

#initialize(seq) ⇒ TestCode

Returns a new instance of TestCode.



9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
 
# File 'lib/full_lengther_next/classes/test_code.rb', line 9

def initialize(seq)
	
	name=''
	t_code=''
	status=''
	ref_start=0
	ref_end=seq.seq_fasta.length
	ref_frame=''
	orf=''
	protein = ''
	p_long = 0
	
	if (seq.fasta_length < 200)
		ref_name = seq.seq_name
		ref_code = 0.0
		ref_frame = 0
		ref_status = 'unknown'
		ref_orf = ''
		ref_msgs = 'Sequence length < 200 nt'
		
		seq.annotate(:tcode_unknown,"#{ref_name}\t#{seq.fasta_length}\t\ttestcode\t#{ref_status}\t#{ref_code}\t\t\t\t\t#{ref_msgs}\t#{ref_frame}\t#{ref_start}\t#{ref_end}\t\t\t\t",true)
		# seq.annotate(:tcode,"#{ref_name}\t#{seq.seq_fasta.length}\t\ttestcode\t#{ref_status}\t#{ref_code}\t\t\t\t\t#{ref_msgs}\t#{ref_frame}\t#{ref_start}\t#{ref_end}\t\t\t\t",true)
	else
		
# para probar tescode con toda la secuencia, en lugar de con los ORFs ----------------------------------------------------------------------
		# sense_strand = seq.seq_fasta.upcase
		# antisense_strand = sense_strand.complementary_dna
		# (t_code,t_status) = testCode_exec(sense_strand)
		# ref_frame = 1
		# ref_msgs = ''
		# (as_t_code,as_t_status) = testCode_exec(antisense_strand)
		# # puts "#{seq.seq_name}: t_code: #{t_code}, t_status: #{t_status}, as_t_code: #{as_t_code}, as_t_status: #{as_t_status}"
		# seq.annotate(:tcode,"#{seq.seq_name}\t#{seq.seq_fasta.length}\t\ttestcode\t#{t_status}\t#{t_code}\t\t\t\t\t#{ref_msgs}\t#{ref_frame}\t#{ref_start}\t#{ref_end}\t\t\t\t",true)
# --------------------------------------------------------------------------------------------------------------------------------


		# see add_region filter
		(name,t_code,status,ref_start,ref_end,ref_frame,orf,ref_msgs,stop_before_start,more_than_one_frame) = t_code(seq)
		if (status == :unknown)
			seq.annotate(:tcode_unknown,"#{name}\t#{seq.fasta_length}\t\ttestcode\t#{status}\t#{t_code}\t\t\t\t\t#{ref_msgs}\t#{ref_frame}\t#{ref_start}\t#{ref_end}\t\t\t\t",true)
		else
			seq.annotate(:tcode,"#{name}\t#{seq.fasta_length}\t\ttestcode\t#{status}\t#{t_code}\t\t\t\t\t#{ref_msgs}\t#{ref_frame}\t#{ref_start}\t#{ref_end}\t\t\t\t",true)
		end
		
		# if (ref_msgs.nil?)
		# 	ref_msgs = ''
		# end
		# 
		# if (stop_before_start)
		# 	ref_msgs += "There is a STOP codon before ATG. "
		# end
		# 
		# if (more_than_one_frame)
		# 	ref_msgs += "Possible frame error by an ins/del"
		# end
		# 
		# if (status.to_s =~ /^[CN]\_terminus/) || (status == :Internal)
		# 	tmp_status = "Putative #{status.to_s}"
		# else
		# 	tmp_status = status.to_s
		# end
		# 
		# 	
		# if (!orf.nil?) && (!more_than_one_frame)
		# 	protein = orf.translate
		# 	p_long = protein.length - 3
		# 	seq.annotate(:tcode,"#{name}\t#{seq.seq_fasta.length}\t\ttestcode\t#{tmp_status}\t#{t_code}\t\t\t#{p_long}\t\t#{ref_msgs}\t#{ref_frame}\t#{ref_start}\t#{ref_end}\t\t\t\t#{protein}",true)
		# else
		# 	seq.annotate(:tcode,"#{name}\t#{seq.seq_fasta.length}\t\ttestcode\t#{tmp_status}\t#{t_code}\t\t\t\t\t#{ref_msgs}\t#{ref_frame}\t#{ref_start}\t#{ref_end}\t\t\t\t",true)
		# end
		
	end
end

Instance Method Details

#add_region(orf_seq, orf_t_start, orf_t_end, orf_frame, orf_stop_codon, orf_type, seq) ⇒ Object

to add regions over a determinated size



221
222
223
224
225
226
227
228
 
# File 'lib/full_lengther_next/classes/test_code.rb', line 221

def add_region(orf_seq, orf_t_start, orf_t_end, orf_frame, orf_stop_codon, orf_type,seq)

	if (orf_seq.length >= 200)
		# puts "#{seq.seq_name}, #{orf_t_start} - #{orf_t_end}, #{orf_frame}, #{orf_type}"
		seq.add_orf(orf_seq, orf_t_start, orf_t_end, orf_frame, orf_stop_codon, orf_type)
	end

end

#calcParam(valueOne, valueTwo, valueThree) ⇒ Object 



778
779
780
781
782
783
784
 
# File 'lib/full_lengther_next/classes/test_code.rb', line 778

def calcParam (valueOne,valueTwo,valueThree)
	paramArray = [valueOne,valueTwo,valueThree];
	paramArray = paramArray.sort#{|a,b| return a-b}#(compareNumbers);				
	paramValue = paramArray[2] / (paramArray[0] + 1.0);
	# puts paramArray.to_json
	return paramValue;
end

#compare_regions(this_strand, tc_fasta) ⇒ Object

para escoger la region codificante mas grande, incluso solapando verios frames



206
207
208
209
210
211
212
213
214
215
216
217
218
 
# File 'lib/full_lengther_next/classes/test_code.rb', line 206

def compare_regions(this_strand,tc_fasta)
	
	# select the largest ORF without frame repair-------------------------------- hay que comentar todo el bloque de arriba
	best_orf = nil
	best_orf = this_strand.sort{|x,y| y.seq.length <=> x.seq.length }[0]
	
	if !best_orf.nil?
		best_orf.type = best_orf.status
	end
	
	return best_orf

end

#compare_regions_old(this_strand, tc_fasta) ⇒ Object

no se usa para escoger la region codificante mas grande, incluso solapando verios frames



627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
 
# File 'lib/full_lengther_next/classes/test_code.rb', line 627

def compare_regions_old(this_strand,tc_fasta)

	# array_regions = []
	# array_regions.push this_strand.first.dup
	# 
	# this_strand.each do |one_orf|
	# 
	# 	prev_orf = array_regions.last.dup # taking last orf before add actual orf
	# 	array_regions.push one_orf.dup # add actual orf, el primer orf me va a salir duplicado
	# 
	# 	if prev_orf.overlaps?(one_orf)
	# 		prev_orf.seq = tc_fasta[prev_orf.t_start..one_orf.t_end]
	# 
	# 		(t_code,t_status)=testCode_exec(prev_orf.seq)
	# 
	# 		prev_orf.score = t_code
	# 		prev_orf.status = t_status
	# 
	# 		#t_start, frame and stop_codon are the same
	# 		prev_orf.t_end = one_orf.t_end
	# 		if (prev_orf.type != one_orf.type)
	# 			prev_orf.type = type_fusion(prev_orf.type,one_orf.type)
	# 		end
	# 		prev_orf.more_than_one_frame = true
	# 
	# 		# puts "overlaps:"
	# 		# puts "#{one_orf.t_start} - #{one_orf.t_end}"
	# 		# puts "#{array_regions.last.t_start} - #{array_regions.last.t_end}"
	# 
	# 		array_regions.push prev_orf # add overlapped orf,
	# 	end
	# 
	# end
	# 
	# # select the largest ORF without frame repair-------------------------------- hay que comentar todo el bloque de arriba
	# # best_orf = nil
	# # best_orf = this_strand.sort{|x,y| y.seq.length <=> x.seq.length }[0]
	# # ---------------------------------------------------------------------------
	# 
	# # select the largest ORF ----------------------------------------------------
	# # best_orf = nil
	# # best_orf = array_regions.sort{|x,y| y.seq.length <=> x.seq.length }[0]
	# # if !best_orf.nil?
	# # 	puts "best_orf.status: #{best_orf.status}, best_orf.type: #{best_orf.type}"
	# # end
	# 
	# 
	# # ---------------------------------------------------------------------------
	# 
	# # select the largest coding ORF ---------------------------------------------
	# best_orf = nil
	# array_regions.sort{|x,y| y.seq.length <=> x.seq.length }.each do |one_orf|
	# 	# puts "#{one_orf.status}, #{one_orf.type}"
	# 	if (one_orf.status == :coding)
	# 		best_orf = one_orf
	# 		break
	# 	end
	# end
	# # ---------------------------------------------------------------------------
	# 
	# # puts "\n\n\nstart"
	# # array_regions.sort{|x,y| y.seq.length <=> x.seq.length }.each do |one_orf|
	# # 	puts one_orf.seq.length
	# # end
	# # puts "end\n\n\n"
	# # puts "best_orf: #{best_orf.seq.length}"
	# 
	# # if !best_orf.nil?
	# # 	best_orf.type = best_orf.status
	# # end
	# 
	# return best_orf

end

#countBases(valueOne, valueTwo, valueThree) ⇒ Object 



786
787
788
 
# File 'lib/full_lengther_next/classes/test_code.rb', line 786

def countBases (valueOne,valueTwo,valueThree)
	return valueOne + valueTwo + valueThree;
end

#generate_uncomplete_orf(a, frame, seq) ⇒ Object

se buscan las regiones Complete, N-terminus, C-terminus e Internal en la secuencia de cada frame



231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
 
# File 'lib/full_lengther_next/classes/test_code.rb', line 231

def generate_uncomplete_orf(a,frame,seq)
	
	my_atg = true
	atg_codon = false
	stop_codon = false
	any_stop = false
	
	orf =''
	t_start = 0
	t_end = 0
	
	a.each do |e|
		t_end += 3
		orf += e
		
		if (e == 'ATG') && (!atg_codon)
			atg_codon = true
			stop_codon = false
			t_start = t_end - 3
		elsif (e == 'TAG') || (e == 'TGA') || (e == 'TAA')
			orf_tmp = orf[t_start..t_end]
			if (any_stop)
				# case 1, complete orf
				if (atg_codon)
					orf_tmp = orf[t_start..t_end]
					add_region(orf_tmp, t_start, t_end, frame, any_stop, :Complete,seq)
				end
			else
				# case 2, C_terminus
				if (my_atg)
					orf_tmp = orf[0..t_end]
					add_region(orf_tmp, 0, t_end, frame, any_stop, :C_terminus,seq)
					# case 3, putative complete, complete without stop codon before atg
					if (atg_codon)
						orf_tmp = orf[t_start..t_end]
						add_region(orf_tmp, t_start, t_end, frame, any_stop, :Complete, seq)
					end
				end
			end
			
			stop_codon = true
			any_stop = true
			my_atg = false
			atg_codon = false
			t_start += 3
		end
	end
	
	# case 4, N_terminus and case 6, putative N_terminus
	if (atg_codon) && (!stop_codon)
		orf_tmp = orf[t_start..t_end]
		add_region(orf_tmp, t_start, t_end, frame, any_stop, :N_terminus,seq)
	end
	
	# case 5, internal
	if (my_atg) && (!any_stop)
		orf_tmp = orf[0..t_end]
		add_region(orf_tmp, 0, t_end, frame, any_stop, :Internal,seq)
	end
	
end

#getConclusion(testCode_value) ⇒ Object 



867
868
869
870
871
872
873
874
875
876
877
878
 
# File 'lib/full_lengther_next/classes/test_code.rb', line 867

def getConclusion (testCode_value)
	codeProb = "";
	if (testCode_value < 0.74)
		codeProb = :unknown;
	elsif (testCode_value >=0.74 and testCode_value < 0.95)
		codeProb = :putative_coding;
	elsif (testCode_value >=0.95)
		codeProb = :coding;
	end

	return codeProb;
end

#orf_fusion(orfs_array, tc_fasta, name, ref_status, ref_code, ref_start, ref_end, ref_frame, ref_orf, ref_msgs) ⇒ Object

no se usa



350
351
352
353
354
355
356
357
358
359
360
361
362
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
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
 
# File 'lib/full_lengther_next/classes/test_code.rb', line 350

def orf_fusion(orfs_array,tc_fasta,name,ref_status,ref_code,ref_start,ref_end,ref_frame,ref_orf,ref_msgs)

	lower_start = 9999
	higher_end = 0
	new_orf = false
	ref_name = name

	# vamos a coger el mejor de referencia (el coding mas largo) 
	# y vamos a poner en el warning los coding que estan en el mismo sentido y no estan contenidos en el mejor
	orfs_array.sort! {|orf1,orf2| orf1[1] <=> orf2[1]}

	tmp_orf = ref_orf
	tmp_start = ref_start
	tmp_end = ref_end
	tmp_frame = ref_frame
	tmp_msg = ''

	# puts "\n\n#{name} ---- tmp_frame: #{tmp_frame} ------------------------ \n\n"

	orfs_array.each do |orf|

		(orf[1],orf[2]) = corrige_frame(orf[3],orf[1],orf[2])
		# (orf[1],orf[2]) = $an.corrige_frame(orf[3],orf[1],orf[2])

		# puts "*** name: #{name}, orf[1]: #{orf[1]}, orf[2]: #{orf[2]}, orf[3]: #{orf[3]} ref_start: #{ref_start}, ref_end: #{ref_end}, ref_frame: #{ref_frame} ***\n\n"

		if (orf[0] != tmp_orf)

			if ((tmp_end >= orf[1]) && (tmp_end <= orf[2])) || ((tmp_start >= orf[1]) && (tmp_start <= orf[2])) # los ORFs solapan

				# puts "SOLAPAN     frame: #{orf[3]}  tmp_start: #{tmp_start} tmp_end: #{tmp_end} orf_start: #{orf[1]} orf_end: #{orf[2]}"
				if (tmp_frame > 0)
					tmp_msg = ", overlapping coding region (#{orf[1]},#{orf[2]})"
				elsif (tmp_frame < 0)
					tmp_msg = ", overlapping coding region (-#{orf[1]},-#{orf[2]})"
				end
				new_orf = true

			elsif (tmp_end < orf[1]) || (tmp_start > orf[2]) # los ORFs estan separados

				# puts "#{name}  frame: #{orf[3]}    SEPARADOS --> tmp_start: #{tmp_start} tmp_end: #{tmp_end} orf_start: #{orf[1]} orf_end: #{orf[2]}"
				if (tmp_frame > 0)
					tmp_msg = ", other coding region (#{orf[1]},#{orf[2]})"
				elsif (tmp_frame < 0)
					tmp_msg = ", other coding region (-#{orf[1]},-#{orf[2]})"
				end
				new_orf = true

			end

			if (new_orf == true)

				if (orf[1] < lower_start)
					lower_start = orf[1]
				end

				# if (orf[2] > higher_end)
				# end

				(tmp_code,tmp_status)=testCode_exec(tc_fasta[lower_start-1..higher_end-1])

				if (tmp_status != 'unknown')
					# puts "#{name} ----------------------------------- FUSION!!!!!!!!!!!!!!!!\n\n"
					# tenemos varios ORFs q son codificantes al unirlos
					ref_msgs += tmp_msg
					new_orf = false
				else
					# puts "#{name} ------------------------------------NO se unen\n\n"
				end
			end
		end
	end
	return[ref_status,ref_code,ref_name,ref_start,ref_end,ref_frame,ref_orf,ref_msgs]
end

#t_code(seq) ⇒ Object 



83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
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
 
# File 'lib/full_lengther_next/classes/test_code.rb', line 83

def t_code(seq)
	
	name = seq.seq_name
	tc_fasta = seq.seq_fasta
	
	# generamos todos los ORFs de cada secuencia
	uncomplete_orf_finder(seq)
	minus_strand = []
	plus_strand = []
	
	# puts "**************************************************"
	# puts "#{name} #{tc_fasta.length}"
	# ordenamos los ORFs empezando desde 5' a 3' y luego separamos los de cada hebra en un array distinto
	seq.orfs.sort{|x,y| x.t_start <=> y.t_start }.each do |one_orf|
		
		(t_code,t_status)=testCode_exec(one_orf.seq)
		one_orf.status = t_status
		one_orf.score = t_code
		
		if (one_orf.frame < 0)
			minus_strand.push one_orf
		elsif (one_orf.frame > 0)
			plus_strand.push one_orf
		end
		
	end
	#----------------------------------- Plus strand
	if (!plus_strand.empty?)
		# puts "--------------Plus strand:"
		best_plus_region = compare_regions(plus_strand,tc_fasta)
		if (!best_plus_region.nil?)
			# puts "#{best_plus_region.seq.length}, #{best_plus_region.status}, #{best_plus_region.type}, #{best_plus_region.t_start} - #{best_plus_region.t_end}, #{best_plus_region.frame}"
			# puts best_plus_region.seq
		end
	end
	#----------------------------------- Minus strand
	if (!minus_strand.empty?)
		# puts "--------------Minus strand:"
		best_minus_region = compare_regions(minus_strand,tc_fasta)
		if (!best_minus_region.nil?)
			# puts "#{best_minus_region.seq.length}, #{best_minus_region.status}, #{best_minus_region.type}, #{best_minus_region.t_start} - #{best_minus_region.t_end}, #{best_minus_region.frame}"
			# puts best_minus_region.seq
		end
	end
	# obtenemos la region codificante mas larga de ambas hebras
	best_region = nil
	if (!best_plus_region.nil?)
		if (!best_minus_region.nil?)
			if (best_minus_region.seq.length > best_plus_region.seq.length)
				best_region = best_minus_region
			else
				best_region = best_plus_region
			end
		else
			best_region = best_plus_region
		end
	elsif (!best_minus_region.nil?)
		best_region = best_minus_region
	end
	# puts "--------------Best region:"
	# puts " --------------------------------- #{best_region.seq.length}, #{best_region.status}, #{best_region.type}, #{best_region.t_start} - #{best_region.t_end}, #{best_region.frame}"
	# comprobamos el tipo de ORF segun si tiene un codon de parada antes del atg

	if (!best_region.nil?) && (best_region.seq.length >= 200)
		if (best_region.type == :Complete) && (!best_region.stop_codon)
			best_region.type = 'Putative Complete'
			ref_msgs = 'NO STOP codon before ATG. '
		elsif (best_region.type == :N_terminus) && (!best_region.stop_codon)
			ref_msgs = 'NO STOP codon before ATG. '
		end
		return [name, best_region.score, best_region.type, best_region.t_start, best_region.t_end, best_region.frame, best_region.seq, ref_msgs, best_region.stop_codon, best_region.more_than_one_frame]
	else
		ref_score = 0.0
		ref_start = 0
		ref_end = 0
		ref_frame = 0
		ref_orf = ''
		ref_type = 'unknown'
		ref_msgs = 'Non coding ORF found >= 200 nt '
		return [name, ref_score, ref_type, ref_start, ref_end, ref_frame, ref_orf, ref_msgs, false, false]
	end
end

#t_code_old(seq) ⇒ Object

no se usa



425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
 
# File 'lib/full_lengther_next/classes/test_code.rb', line 425

def t_code_old(seq)

	ref_code = 0.0
	ref_name = ''
	ref_start = 0
	ref_end = 0
	ref_frame = 0
	ref_status = ''
	ref_orf = ''
	ref_msgs = ''

	name = seq.seq_name
	tc_fasta = seq.seq_fasta
	
	# generamos todos los ORFs mayores de 200pb de cada secuencia, en fl_string_utils
	orfs_array = tc_fasta.orf_finder
	
	if (orfs_array[0].nil?)
		ref_name = name
		ref_code = 0.0
		ref_start = 0
		ref_end = 0
		ref_frame = 0
		ref_status = 'unknown'
		ref_orf = ''
		ref_msgs = 'ORF length < 200 nt'
		# ref_msgs = 'Your sequence has not an ORF longer than 200 nt'

	else
		one_good_orf_minus = false
		more_than_one_minus = false
		one_good_orf_plus = false
		more_than_one_plus = false

		good_orfs_minus = []
		good_orfs_plus = []

		one_coding = false
		one_putative = false

		# orfs_array.sort! {|orf1,orf2| (orf1[2] - orf1[1]) <=> (orf2[2] - orf2[1])}
		orfs_array.each do |orf|

			# long = orf.length - 1
			if (orf[0])
			# if (long >= 200)
				(t_code,t_status)=testCode_exec(orf[0])
#						puts "name: #{name},t_status: #{t_status}, t_code: #{t_code}, stop_codon: #{orf[4]}, length: #{tc_fasta.length}, start: #{orf[1]}, end: #{orf[2]}, frame: #{orf[3]}\n\n"

				if (t_status != 'unknown')
					if (orf[3].to_i < 0)
						if (one_good_orf_minus == true)
							more_than_one_minus = true
							orf.push t_code
							orf.push t_status
							good_orfs_minus.push orf
						else
							one_good_orf_minus = true
							orf.push t_code #orf[5]
							orf.push t_status #orf[6]
							good_orfs_minus.push orf
						end
					elsif (orf[3].to_i > 0)
						if (one_good_orf_plus == true)
							more_than_one_plus = true
							orf.push t_code
							orf.push t_status
							good_orfs_plus.push orf
						else
							one_good_orf_plus = true
							orf.push t_code #orf[5]
							orf.push t_status #orf[6]
							good_orfs_plus.push orf
						end
					end
				end

				# if (t_code.to_f > ref_code) # cogemos el de mejor testcode
				# puts "name: #{name}, orf[0].length: #{orf[0].length}, ref_orf.length: #{ref_orf.length}, t_status: #{t_status}, one_coding: #{one_coding}\n\n"
				if (orf[0].length > ref_orf.length) and (t_status == 'coding') # cogemos el mayor de los coding
					# puts "compleeeeeeeeeeeeeeetttttttttttaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa"
					ref_code = t_code.to_f
					ref_name = name
					ref_orf = orf[0]
					ref_start = orf[1]
					ref_end = orf[2]
					ref_frame = orf[3]

					one_coding = true
					(ref_status,ref_msgs) = checking_beginning(orf[4],t_status,orf[1],tc_fasta,orf[2])

				elsif (one_coding == false) and (orf[0].length > ref_orf.length) and (t_status == 'putative_coding')
					# puts "putaaaaaaaaaaaaaaaaaaativeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee"
					ref_code = t_code.to_f
					ref_name = name
					ref_orf = orf[0]
					ref_start = orf[1]
					ref_end = orf[2]
					ref_frame = orf[3]

					one_putative = true
					(ref_status,ref_msgs) = checking_beginning(orf[4],t_status,orf[1],tc_fasta,orf[2])

				elsif (one_coding == false) and (one_putative == false)
					# puts "unknoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooown"
					ref_status = t_status
					ref_code = t_code.to_f
					ref_name = name
					ref_orf = orf[0]
					ref_start = orf[1]
					ref_end = orf[2]
					ref_frame = orf[3]

					ref_msgs = 'Bad testcode score'
					# ref_msgs = 'test code did not find a coding region in your sequence'
				end
				# puts "**name: #{name},ref_status: #{ref_status}, ref_code: #{ref_code}, length: #{tc_fasta.length}, ref_start: #{ref_start}, ref_end: #{ref_end}, ref_frame: #{ref_frame}\n\n"
				# puts "t_code: #{t_code}, t_status: #{t_status}"
			end
		end

		# vamos a preparar el mejor ORF y devolverlo
		(ref_start,ref_end) = corrige_frame(ref_frame,ref_start,ref_end)
		# puts "**name: #{name}, ref_start: #{ref_start}, ref_end: #{ref_end}, ref_frame: #{ref_frame}\n\n"
		
		# si encontramos más de un orf valido
		if (more_than_one_plus) or (more_than_one_minus)
			if (ref_frame > 0)
				if (more_than_one_plus)
					(ref_status,ref_code,ref_name,ref_start,ref_end,ref_frame,ref_orf,ref_msgs) = orf_fusion(good_orfs_plus,tc_fasta,name,ref_status,ref_code,ref_start,ref_end,ref_frame,ref_orf,ref_msgs)
					# if (ref_frame == 0)
					# 	ref_frame = 7
					# end
					# puts "merging ORFs with orf_fusion!!!!"
				end
			elsif (ref_frame < 0)
				if (more_than_one_minus)
					(ref_status,ref_code,ref_name,ref_start,ref_end,ref_frame,ref_orf,ref_msgs) = orf_fusion(good_orfs_minus,tc_fasta,name,ref_status,ref_code,ref_start,ref_end,ref_frame,ref_orf,ref_msgs)
					# if (ref_frame == 0)
					# 	ref_frame = -7
					# end
					# puts "merging ORFs with orf_fusion!!!!"
				end
			end
		end

		# puts "name: #{name},t_status: #{ref_status}, t_code: #{ref_code}, frame: #{ref_frame},start: #{ref_start}, end: #{ref_end}\n\n"

		if (ref_frame < 0)
			(kk1,kk2,ref_start2,ref_end2) = reverse_seq(tc_fasta,ref_frame,ref_start,ref_end)

			ref_start_ok = "#{ref_start2} (-#{ref_start})"
			ref_end_ok = "#{ref_end2} (-#{ref_end})"
		else
			ref_start_ok = ref_start
			ref_end_ok = ref_end
		end
	end

		return [ref_name,ref_code,ref_status,ref_start_ok,ref_end_ok,ref_frame,ref_orf,ref_msgs]

end

#testCode_exec(sequence) ⇒ Object

test code program functions #########



704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
 
# File 'lib/full_lengther_next/classes/test_code.rb', line 704

def testCode_exec (sequence)

	sequence.downcase!
	basesOne = [0,0,0,0];
	basesTwo = [0,0,0,0];
	basesThree = [0,0,0,0];

	#for (j = 0; j < sequence.length; j = j + 3)

	0.step(sequence.length-1,3) do |j|
		if (sequence[j].chr == "g")
			basesOne[0] = basesOne[0] + 1;
		elsif (sequence[j].chr == "a")
			basesOne[1] = basesOne[1] + 1;
		elsif (sequence[j].chr == "t")
			basesOne[2] = basesOne[2] + 1;
		elsif (sequence[j].chr == "c")
			basesOne[3] = basesOne[3] + 1;
		else
		end
	end

					#for (j = 1; j < sequence.length; j = j + 3)
	1.step(sequence.length-1,3) do |j|
		if (sequence[j].chr == "g")
			basesTwo[0] = basesTwo[0] + 1;
		elsif (sequence[j].chr == "a")
			basesTwo[1] = basesTwo[1] + 1;
		elsif (sequence[j].chr == "t")
			basesTwo[2] = basesTwo[2] + 1;
		elsif (sequence[j].chr == "c")
			basesTwo[3] = basesTwo[3] + 1;
		else
		end
	end


	#for (j = 2; j < sequence.length; j = j + 3)
	2.step(sequence.length-1,3) do |j|
		if (sequence[j].chr == "g")
			basesThree[0] = basesThree[0] + 1;
		elsif (sequence[j].chr == "a")
			basesThree[1] = basesThree[1] + 1;
		elsif (sequence[j].chr == "t")
			basesThree[2] = basesThree[2] + 1;
		elsif (sequence[j].chr == "c")
			basesThree[3] = basesThree[3] + 1;
		else
		end
	end

	paramG = calcParam(basesOne[0],basesTwo[0],basesThree[0]);
	contentG = countBases(basesOne[0],basesTwo[0],basesThree[0]) / sequence.length.to_f;
	posProbG = usePosParam(paramG,"g");
	contProbG = useContParam(contentG,"g");
	paramA = calcParam(basesOne[1],basesTwo[1],basesThree[1]);
	contentA = countBases(basesOne[1],basesTwo[1],basesThree[1]) / sequence.length.to_f;
	posProbA = usePosParam(paramA,"a");
	contProbA = useContParam(contentA,"a");
	paramT = calcParam(basesOne[2],basesTwo[2],basesThree[2]);
	contentT = countBases(basesOne[2],basesTwo[2],basesThree[2]) / sequence.length.to_f;
	posProbT = usePosParam(paramT,"t");
	contProbT = useContParam(contentT,"t");
	paramC = calcParam(basesOne[3],basesTwo[3],basesThree[3]);
	contentC = countBases(basesOne[3],basesTwo[3],basesThree[3]) / sequence.length.to_f;
	posProbC = usePosParam(paramC,"c");
	contProbC = useContParam(contentC,"c");
	valueY = posProbG * 0.31 + contProbG * 0.15 + posProbA * 0.26 + contProbA * 0.11 + posProbT * 0.33 + contProbT * 0.14 + posProbC * 0.18 + contProbC * 0.12;
	valueY = ((valueY*1000.0).round/1000.0);

	# return 'The TestCode value is <b>' + valueY.to_s + '</b>, which indicates that the sequence ' + getConclusion(valueY) + '.';
	return [valueY.to_s, getConclusion(valueY)]
end

#type_fusion(prev_type, one_type) ⇒ Object

cuando se unen dos regiones de diferentes frames, nos dice de que tipo es la union, Complete, Internal, N-terminus…



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
 
# File 'lib/full_lengther_next/classes/test_code.rb', line 167

def type_fusion(prev_type,one_type)
	res_type = :Internal
	if (prev_type == :C_terminus) #-------------- C-terminus
			if (one_type == :N_terminus)
				res_type = :Internal
			elsif (one_type == :Internal)
				res_type = :Internal
			elsif (one_type == :Complete)
				res_type = :C_terminus
			end
	elsif (prev_type == :N_terminus) #-------------- N-terminus
		if (one_type == :C_terminus)
			res_type = :Complete
		elsif (one_type == :Internal)
			res_type = :N_terminus
		elsif (one_type == :Complete)
			res_type = :Complete
		end
	elsif (prev_type == :Internal) #-------------- Internal
		if (one_type == :C_terminus)
			res_type = :C_terminus
		elsif (one_type == :N_terminus)
			res_type = :Internal
		elsif (one_type == :Complete)
			res_type = :C_terminus
		end
	elsif (prev_type == :Complete) #-------------- Complete
		if (one_type == :C_terminus)
			res_type = :Complete
		elsif (one_type == :N_terminus)
			res_type = :N_terminus
		elsif (one_type == :Internal)
			res_type = :N_terminus
		end
	end
	return res_type
end

#uncomplete_orf_finder(seq) ⇒ Object

recorre cada uno de los frames y los pasa a generate_uncomplete_orf



294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
 
# File 'lib/full_lengther_next/classes/test_code.rb', line 294

def uncomplete_orf_finder(seq)
	
	s = seq.seq_fasta.upcase
	f1 = s.split('').each_slice(3).map{|e| e.join}
	generate_uncomplete_orf(f1,1,seq)
	
	s.sub!(/^./,'')
	f2 = s.split('').each_slice(3).map{|e| e.join}
	generate_uncomplete_orf(f2,2,seq)
	
	s.sub!(/^./,'')
	f3 = s.split('').each_slice(3).map{|e| e.join}
	generate_uncomplete_orf(f3,3,seq)
	
	# vamos a por los ORFs de la cadena complementaria
	s = seq.seq_fasta.upcase
	s = s.complementary_dna
	
	f4 = s.split('').each_slice(3).map{|e| e.join}
	generate_uncomplete_orf(f4,-1,seq)
	
	s.sub!(/^./,'')
	f5 = s.split('').each_slice(3).map{|e| e.join}
	generate_uncomplete_orf(f5,-2,seq)
	
	s.sub!(/^./,'')
	f6 = s.split('').each_slice(3).map{|e| e.join}
	generate_uncomplete_orf(f6,-3,seq)
	
end

#useContParam(paramValue, base) ⇒ Object 



829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
 
# File 'lib/full_lengther_next/classes/test_code.rb', line 829

def useContParam (paramValue,base)
	arrayOfCodingProb = [];
	codeProb = 0;
	if (base == "g")
		arrayOfCodingProb = [0.29,0.33,0.41,0.41,0.73,0.64,0.64,0.47,0.54,0.40]
	elsif (base == "a")
		arrayOfCodingProb = [0.21,0.81,0.65,0.67,0.49,0.62,0.55,0.44,0.49,0.28]
	elsif (base == "t")
		arrayOfCodingProb = [0.58,0.51,0.69,0.56,0.75,0.55,0.40,0.39,0.24,0.28]
	elsif (base == "c")
		arrayOfCodingProb = [0.31,0.39,0.44,0.43,0.59,0.59,0.64,0.51,0.64,0.82]
	end

	if (paramValue >= 0 and paramValue < 0.17)
		codeProb = arrayOfCodingProb[0];
	elsif (paramValue >=0.17 and paramValue < 0.19)
		codeProb = arrayOfCodingProb[1];
	elsif (paramValue >=0.19 and paramValue < 0.21)
		codeProb = arrayOfCodingProb[2];
	elsif (paramValue >=0.21 and paramValue < 0.23)
		codeProb = arrayOfCodingProb[3];
	elsif (paramValue >=0.23 and paramValue < 0.25)
		codeProb = arrayOfCodingProb[4];
	elsif (paramValue >=0.25 and paramValue < 0.27)
		codeProb = arrayOfCodingProb[5];
	elsif (paramValue >=0.27 and paramValue < 0.29)
		codeProb = arrayOfCodingProb[6];
	elsif (paramValue >=0.29 and paramValue < 0.31)
		codeProb = arrayOfCodingProb[7];
	elsif (paramValue >=0.31 and paramValue < 0.33)
		codeProb = arrayOfCodingProb[8];
	elsif (paramValue >=0.33)
		codeProb = arrayOfCodingProb[9];
	end

	return codeProb;
end

#usePosParam(paramValue, base) ⇒ Object 



790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
 
# File 'lib/full_lengther_next/classes/test_code.rb', line 790

def usePosParam (paramValue,base)
	arrayOfCodingProb = [];
	codeProb = 0;
	if (base == "g")
		arrayOfCodingProb = [0.08,0.08,0.16,0.27,0.48,0.53,0.64,0.74,0.88,0.90]
	elsif (base == "a")
		arrayOfCodingProb = [0.22,0.20,0.34,0.45,0.68,0.58,0.93,0.84,0.68,0.94]
	elsif (base == "t")
		arrayOfCodingProb = [0.09,0.09,0.20,0.54,0.44,0.69,0.68,0.91,0.97,0.97]
	elsif (base == "c")
		arrayOfCodingProb = [0.23,0.30,0.33,0.51,0.48,0.66,0.81,0.70,0.70,0.80]
	end


	if (paramValue >= 0 and paramValue < 1.1)
		codeProb = arrayOfCodingProb[0];
	elsif (paramValue >=1.1 and paramValue < 1.2)
		codeProb = arrayOfCodingProb[1];
	elsif (paramValue >=1.2 and paramValue < 1.3)
		codeProb = arrayOfCodingProb[2];
	elsif (paramValue >=1.3 and paramValue < 1.4)
		codeProb = arrayOfCodingProb[3];
	elsif (paramValue >=1.4 and paramValue < 1.5)
		codeProb = arrayOfCodingProb[4];
	elsif (paramValue >=1.5 and paramValue < 1.6)
		codeProb = arrayOfCodingProb[5];
	elsif (paramValue >=1.6 and paramValue < 1.7)
		codeProb = arrayOfCodingProb[6];
	elsif (paramValue >=1.7 and paramValue < 1.8)
		codeProb = arrayOfCodingProb[7];
	elsif (paramValue >=1.8 and paramValue < 1.9)
		codeProb = arrayOfCodingProb[8];
	elsif (paramValue >=1.9)
		codeProb = arrayOfCodingProb[9];
	end

	return codeProb;
end

#window_walking(seq) ⇒ Object

gnuplot must be installed



589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
 
# File 'lib/full_lengther_next/classes/test_code.rb', line 589

def window_walking(seq)
	
	tcode_array = []
	y1=[]
	y2=[]
	
	s = seq.seq_fasta.upcase
	(s.length-200).times do |i|
		(t_code,t_status)=testCode_exec(s[i..i+199])
		y1.push t_code
	end
	
	tcode_array_rc = []
	
	src = s.complementary_dna
	(src.length-200).times do |i|
		(t_code,t_status)=testCode_exec(src[i..i+199])
		# puts "#{i}-#{i+199}"
		# puts t_status
		# puts t_code
		puts src[i..i+199]
		y2.push t_code
	end
	
	# Create lines plot
  p=ScbiPlot::Lines.new('lines.png','title')
  x=(1..src.length-200).entries
  p.add_x(x)
	
	# puts "x_length: #{src.length-200} #{x}"
	# puts "x: #{x.length}, y: #{y1.length}"
	p.add_series('serie0', y1)

	p.do_graph
	
end