macroape 3.3.5 → 3.3.6

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Files changed (11) hide show
  1. data/lib/macroape.rb +0 -1
  2. data/lib/macroape/cli/preprocess_collection.rb +9 -6
  3. data/lib/macroape/cli/scan_collection.rb +14 -17
  4. data/lib/macroape/version.rb +1 -1
  5. data/macroape.gemspec +2 -2
  6. data/test/data/test_collection.yaml +57 -47
  7. data/test/data/test_collection_single_file.txt +25 -25
  8. data/test/data/test_collection_single_file_pcm.txt +26 -26
  9. data/test/test_helper.rb +8 -7
  10. metadata +4 -5
  11. data/lib/macroape/collection.rb +0 -22
data/lib/macroape.rb CHANGED
@@ -6,7 +6,6 @@ require 'macroape/counting'
6
6
  require 'macroape/aligned_pair_intersection'
7
7
  require 'macroape/pwm_compare_aligned'
8
8
  require 'macroape/pwm_compare'
9
- require 'macroape/collection'
10
9
 
11
10
  module Macroape
12
11
  # Your code goes here...
data/lib/macroape/cli/preprocess_collection.rb CHANGED
@@ -71,10 +71,13 @@ module Macroape
71
71
  end
72
72
  pvalues = default_pvalues if pvalues.empty?
73
73
 
74
- collection = Macroape::Collection.new(rough_discretization, precise_discretization, background, pvalues)
74
+ collection = Bioinform::Collection.new(rough_discretization: rough_discretization,
75
+ precise_discretization: precise_discretization,
76
+ background: background,
77
+ pvalues: pvalues)
75
78
 
76
79
  if File.directory?(data_source)
77
- motifs = Dir.glob(File.join(data_source,'*')).map do |filename|
80
+ motifs = Dir.glob(File.join(data_source,'*')).sort.map do |filename|
78
81
  pwm = data_model.new(File.read(filename))
79
82
  pwm.name ||= File.basename(filename, File.extname(filename))
80
83
  pwm
@@ -98,18 +101,18 @@ module Macroape
98
101
  # Otherwise it should skip motif and tell you about this
99
102
  # Also two command line options to fail on skipping or to skip silently should be included
100
103
 
101
- info = {rough: {}, precise: {}}
104
+ info = OpenStruct.new(rough: {}, precise: {})
102
105
  pwm.background!(background).max_hash_size!(max_hash_size)
103
106
 
104
107
  pwm.discrete(rough_discretization).thresholds(*pvalues) do |pvalue, threshold, real_pvalue|
105
- info[:rough][pvalue] = threshold / rough_discretization
108
+ info.rough[pvalue] = threshold / rough_discretization
106
109
  end
107
110
 
108
111
  pwm.discrete(precise_discretization).thresholds(*pvalues) do |pvalue, threshold, real_pvalue|
109
- info[:precise][pvalue] = threshold / precise_discretization
112
+ info.precise[pvalue] = threshold / precise_discretization
110
113
  end
111
114
 
112
- collection.add_pwm(pwm, info)
115
+ collection.add_pm(pwm, info)
113
116
  end
114
117
  File.open(output_file,'w') do |f|
115
118
  f.puts(collection.to_yaml)
data/lib/macroape/cli/scan_collection.rb CHANGED
@@ -46,7 +46,7 @@ module Macroape
46
46
  pvalue = 0.0005
47
47
  cutoff = 0.05 # minimal similarity to output
48
48
  collection = YAML.load_file(collection_file)
49
- background_query = collection.background
49
+ background_query = collection.parameters.background
50
50
  max_hash_size = 1000000
51
51
  max_pair_hash_size = 1000
52
52
 
@@ -80,7 +80,7 @@ module Macroape
80
80
  end
81
81
  end
82
82
 
83
- raise "Thresholds for pvalue #{pvalue} aren't presented in collection (#{collection.pvalues.join(', ')}). Use one of listed pvalues or recalculate the collection with needed pvalue" unless collection.pvalues.include? pvalue
83
+ raise "Thresholds for pvalue #{pvalue} aren't presented in collection (#{collection.parameters.pvalues.join(', ')}). Use one of listed pvalues or recalculate the collection with needed pvalue" unless collection.parameters.pvalues.include? pvalue
84
84
 
85
85
  if filename == '.stdin'
86
86
  query_input = $stdin.read
@@ -92,8 +92,8 @@ module Macroape
92
92
  query_pwm = data_model.new(query_input).to_pwm
93
93
  query_pwm.background(background_query).max_hash_size(max_hash_size)
94
94
 
95
- query_pwm_rough = query_pwm.discrete(collection.rough_discretization)
96
- query_pwm_precise = query_pwm.discrete(collection.precise_discretization)
95
+ query_pwm_rough = query_pwm.discrete(collection.parameters.rough_discretization)
96
+ query_pwm_precise = query_pwm.discrete(collection.parameters.precise_discretization)
97
97
 
98
98
  query_threshold_rough = query_pwm_rough.threshold(pvalue)
99
99
  query_threshold_precise = query_pwm_precise.threshold(pvalue)
@@ -101,19 +101,16 @@ module Macroape
101
101
  similarities = {}
102
102
  precision_file_mode = {}
103
103
 
104
- collection.pwms.each_key do |name|
105
- pwm = collection.pwms[name]
106
- pwm.background(collection.background).max_hash_size(max_hash_size)
107
- pwm_rough = pwm.discrete(collection.rough_discretization)
108
- pwm_precise = pwm.discrete(collection.precise_discretization)
109
-
110
- pwm_info = collection.infos[name]
111
-
112
- pwm_threshold_rough = pwm_info[:rough][pvalue] * collection.rough_discretization
113
- pwm_threshold_precise = pwm_info[:precise][pvalue] * collection.precise_discretization
114
-
115
-
116
- STDERR.puts pwm.name unless silent
104
+ collection.each do |pwm, pwm_info|
105
+ name = pwm.name
106
+ pwm.background(collection.parameters.background).max_hash_size(max_hash_size)
107
+ pwm_rough = pwm.discrete(collection.parameters.rough_discretization)
108
+ pwm_precise = pwm.discrete(collection.parameters.precise_discretization)
109
+
110
+ pwm_threshold_rough = pwm_info.rough[pvalue] * collection.parameters.rough_discretization
111
+ pwm_threshold_precise = pwm_info.precise[pvalue] * collection.parameters.precise_discretization
112
+
113
+ STDERR.puts name unless silent
117
114
  cmp = Macroape::PWMCompare.new(query_pwm_rough, pwm_rough).max_hash_size(max_pair_hash_size)
118
115
  info = cmp.jaccard(query_threshold_rough, pwm_threshold_rough)
119
116
  precision_file_mode[name] = :rough
data/lib/macroape/version.rb CHANGED
@@ -1,3 +1,3 @@
1
1
  module Macroape
2
- VERSION = "3.3.5"
2
+ VERSION = "3.3.6"
3
3
  end
data/macroape.gemspec CHANGED
@@ -8,12 +8,12 @@ Gem::Specification.new do |gem|
8
8
  gem.summary = %q{PWM comparison tool using MACROAPE approach}
9
9
  gem.homepage = "http://autosome.ru/macroape/"
10
10
 
11
- gem.files = `git ls-files`.split($\)
11
+ gem.files = `git ls-files`.split($/)
12
12
  gem.executables = gem.files.grep(%r{^bin/}).map{ |f| File.basename(f) }
13
13
  gem.test_files = gem.files.grep(%r{^(test|spec|features)/})
14
14
  gem.name = "macroape"
15
15
  gem.require_paths = ["lib"]
16
16
  gem.version = Macroape::VERSION
17
17
 
18
- gem.add_dependency('bioinform', '>= 0.1.5')
18
+ gem.add_dependency('bioinform', '>= 0.1.7')
19
19
  end
data/test/data/test_collection.yaml CHANGED
@@ -1,17 +1,6 @@
1
- --- !ruby/object:Macroape::Collection
2
- pvalues:
3
- - 0.0005
4
- - 0.0001
5
- - 5.0e-05
6
- background: &17959680
7
- - 1
8
- - 1
9
- - 1
10
- - 1
11
- precise_discretization: 10
12
- rough_discretization: 1
13
- pwms:
14
- GABPA_f1: !ruby/object:Bioinform::PWM
1
+ --- &18156900 !ruby/object:Bioinform::Collection
2
+ collection:
3
+ - - !ruby/object:Bioinform::PWM
15
4
  matrix:
16
5
  - - -0.1106670158341858
17
6
  - 0.013801606113892391
@@ -66,9 +55,25 @@ pwms:
66
55
  - 0.4381106695354074
67
56
  - -1.0304105539540915
68
57
  name: GABPA_f1
69
- background: *17959680
58
+ tags:
59
+ - *18156900
60
+ background: &18124572
61
+ - 1
62
+ - 1
63
+ - 1
64
+ - 1
70
65
  max_hash_size: 1000000
71
- KLF4_f2: !ruby/object:Bioinform::PWM
66
+ - !ruby/object:OpenStruct
67
+ table:
68
+ :rough:
69
+ 5.0e-05: 16.1
70
+ 0.0001: 15.1
71
+ 0.0005: 12.1
72
+ :precise:
73
+ 5.0e-05: 8.61
74
+ 0.0001: 7.609999999999999
75
+ 0.0005: 4.51
76
+ - - !ruby/object:Bioinform::PWM
72
77
  matrix:
73
78
  - - 0.30861857265872605
74
79
  - -2.254321000121579
@@ -111,9 +116,21 @@ pwms:
111
116
  - -0.8080773665408135
112
117
  - -0.18161647647456935
113
118
  name: KLF4_f2
114
- background: *17959680
119
+ tags:
120
+ - *18156900
121
+ background: *18124572
115
122
  max_hash_size: 1000000
116
- SP1_f1: !ruby/object:Bioinform::PWM
123
+ - !ruby/object:OpenStruct
124
+ table:
125
+ :rough:
126
+ 5.0e-05: 14.1
127
+ 0.0001: 13.1
128
+ 0.0005: 11.1
129
+ :precise:
130
+ 5.0e-05: 8.51
131
+ 0.0001: 7.909999999999999
132
+ 0.0005: 5.8100000000000005
133
+ - - !ruby/object:Bioinform::PWM
117
134
  matrix:
118
135
  - - -0.24435707885585292
119
136
  - -0.674823404693731
@@ -160,33 +177,26 @@ pwms:
160
177
  - -0.2862677570028208
161
178
  - -0.68254820978656
162
179
  name: SP1_f1
163
- background: *17959680
180
+ tags:
181
+ - *18156900
182
+ background: *18124572
164
183
  max_hash_size: 1000000
165
- infos:
166
- GABPA_f1:
167
- :rough:
168
- 5.0e-05: 16.1
169
- 0.0001: 15.1
170
- 0.0005: 12.1
171
- :precise:
172
- 5.0e-05: 8.61
173
- 0.0001: 7.609999999999999
174
- 0.0005: 4.51
175
- KLF4_f2:
176
- :rough:
177
- 5.0e-05: 14.1
178
- 0.0001: 13.1
179
- 0.0005: 11.1
180
- :precise:
181
- 5.0e-05: 8.51
182
- 0.0001: 7.909999999999999
183
- 0.0005: 5.8100000000000005
184
- SP1_f1:
185
- :rough:
186
- 5.0e-05: 14.1
187
- 0.0001: 14.1
188
- 0.0005: 11.1
189
- :precise:
190
- 5.0e-05: 8.51
191
- 0.0001: 7.709999999999999
192
- 0.0005: 5.61
184
+ - !ruby/object:OpenStruct
185
+ table:
186
+ :rough:
187
+ 5.0e-05: 14.1
188
+ 0.0001: 14.1
189
+ 0.0005: 11.1
190
+ :precise:
191
+ 5.0e-05: 8.51
192
+ 0.0001: 7.709999999999999
193
+ 0.0005: 5.61
194
+ parameters: !ruby/object:OpenStruct
195
+ table:
196
+ :rough_discretization: 1
197
+ :precise_discretization: 10
198
+ :background: *18124572
199
+ :pvalues:
200
+ - 0.0005
201
+ - 0.0001
202
+ - 5.0e-05
data/test/data/test_collection_single_file.txt CHANGED
@@ -1,28 +1,4 @@
1
- > SP1_f1
2
- -0.24435707885585292 -0.674823404693731 0.8657012535789866 -1.1060188862599287
3
- -1.0631255752097797 -2.111925969423868 1.0960627561110403 -0.6138563775211977
4
- -0.3872276234760535 -2.9739851913218045 1.1807800242010378 -4.338927525031566
5
- -4.563896055436894 -2.9161633002532277 1.3684371349982638 -5.077972423609655
6
- -2.2369752892820083 -3.7196436313301846 1.3510439136452734 -4.889930670508233
7
- -0.07473964149330865 0.944919654762011 -2.6246857648086044 -0.8510983487822436
8
- -1.9643526491643322 -2.978402770880115 1.3113096718240573 -2.324334259499025
9
- -4.0155484139655835 -3.1384268078096667 1.3387488589788057 -2.084673903537648
10
- -0.44509385828355363 -2.2510053061629702 1.1265431574368685 -1.7780413702431372
11
- -1.1896356092245048 -1.2251832285630027 1.1636760063747527 -1.6080243648157353
12
- -0.5166047365590571 0.7641033353626657 -0.2862677570028208 -0.68254820978656
13
- KLF4_f2
14
- 0.30861857265872605 -2.254321000121579 0.13505703522674192 0.3285194224375633
15
- -1.227018967707036 -4.814127713368663 1.3059890687390967 -4.908681463544344
16
- -2.443469374521196 -4.648238485031404 1.3588686548279805 -4.441801801188402
17
- -2.7177827948276123 -3.8073538975356565 1.356272809724262 -3.504104725510225
18
- -0.5563232977367343 0.5340697765121405 -3.61417723090579 0.5270259776377405
19
- -1.8687622060887386 -4.381483976582316 1.337932245336098 -3.815629658877517
20
- -2.045671123823928 -2.384975142213679 0.7198551207724355 0.5449254135616948
21
- -1.373157530374372 -3.0063112097748217 1.285188335493552 -2.5026044231773543
22
- -2.1030513122772208 -1.8941348100402244 1.249265758393991 -1.4284210948906104
23
- -1.3277128628152939 0.8982415633049462 -0.8080773665408135 -0.18161647647456935
24
-
25
- GABPA_f1
1
+ > GABPA_f1
26
2
  -0.1106670158341858 0.013801606113892391 0.6054596108973699 -1.3518085041421573
27
3
  0.37030668921643345 0.15761121480429963 0.009069314183831202 -0.9888619717703562
28
4
  0.47526546359546684 -0.3011678534572083 0.4031522994412777 -1.8638752827041059
@@ -36,3 +12,27 @@ GABPA_f1
36
12
  -1.3716559438167257 -0.2761401935045069 -1.8504445165866068 1.0404320473626856
37
13
  -0.5440863133031895 -0.48103682561971345 0.907381908447086 -1.1280642594012078
38
14
  0.10557340209290218 -0.01814819455289191 0.4381106695354074 -1.0304105539540915
15
+
16
+ KLF4_f2
17
+ 0.30861857265872605 -2.254321000121579 0.13505703522674192 0.3285194224375633
18
+ -1.227018967707036 -4.814127713368663 1.3059890687390967 -4.908681463544344
19
+ -2.443469374521196 -4.648238485031404 1.3588686548279805 -4.441801801188402
20
+ -2.7177827948276123 -3.8073538975356565 1.356272809724262 -3.504104725510225
21
+ -0.5563232977367343 0.5340697765121405 -3.61417723090579 0.5270259776377405
22
+ -1.8687622060887386 -4.381483976582316 1.337932245336098 -3.815629658877517
23
+ -2.045671123823928 -2.384975142213679 0.7198551207724355 0.5449254135616948
24
+ -1.373157530374372 -3.0063112097748217 1.285188335493552 -2.5026044231773543
25
+ -2.1030513122772208 -1.8941348100402244 1.249265758393991 -1.4284210948906104
26
+ -1.3277128628152939 0.8982415633049462 -0.8080773665408135 -0.18161647647456935
27
+ SP1_f1
28
+ -0.24435707885585292 -0.674823404693731 0.8657012535789866 -1.1060188862599287
29
+ -1.0631255752097797 -2.111925969423868 1.0960627561110403 -0.6138563775211977
30
+ -0.3872276234760535 -2.9739851913218045 1.1807800242010378 -4.338927525031566
31
+ -4.563896055436894 -2.9161633002532277 1.3684371349982638 -5.077972423609655
32
+ -2.2369752892820083 -3.7196436313301846 1.3510439136452734 -4.889930670508233
33
+ -0.07473964149330865 0.944919654762011 -2.6246857648086044 -0.8510983487822436
34
+ -1.9643526491643322 -2.978402770880115 1.3113096718240573 -2.324334259499025
35
+ -4.0155484139655835 -3.1384268078096667 1.3387488589788057 -2.084673903537648
36
+ -0.44509385828355363 -2.2510053061629702 1.1265431574368685 -1.7780413702431372
37
+ -1.1896356092245048 -1.2251832285630027 1.1636760063747527 -1.6080243648157353
38
+ -0.5166047365590571 0.7641033353626657 -0.2862677570028208 -0.68254820978656
data/test/data/test_collection_single_file_pcm.txt CHANGED
@@ -1,28 +1,4 @@
1
- > SP1_f1
2
- 682.6436366358055 443.1455214015781 2075.655346294993 287.211468117951
3
- 299.8883246804867 103.74338315843572 2613.8927022405364 471.1315623708902
4
- 591.4892493324709 42.631827541794564 2845.1654083148564 9.36948726124641
5
- 7.071084742361592 45.29093411231232 3432.8847704374107 3.409183158303573
6
- 91.308984085713 19.1536481364332 3373.656949880137 4.5363903481026
7
- 809.2082973387932 2246.941954176211 61.30766021687515 371.19806071846244
8
- 120.56476435866055 42.4349244403591 3242.1560628684038 83.50022078295852
9
- 13.72524477409959 35.858220519297525 3332.4066864946167 106.66582066236779
10
- 558.1188080161639 90.0084504200356 2694.854973210736 145.67374080342415
11
- 264.0088462230318 254.7175868081866 2796.88087480315 173.0486646159857
12
- 519.46013914282 1874.9349086474765 654.5411208373813 439.7198038226514
13
- KLF4_f2
14
- 1233.46088405354 93.18173277811673 1036.6014857092885 1258.2948629970272
15
- 263.979242343185 5.314520555872139 3347.5949971525274 4.650205486388122
16
- 76.7700780003465 6.643150694840173 3529.4896409394937 8.636095903292224
17
- 57.86097393406657 18.102585643439472 3520.3342027139347 25.24120324653207
18
- 518.1947904009378 1545.9062946905135 22.396758181071043 1535.0411222654507
19
- 137.98151691820345 9.300410972776241 3456.320530770924 17.936506876068467
20
- 115.27647661640499 81.51802997128804 1861.9425868567278 1562.801872093553
21
- 227.8095486111286 42.84555258785854 3278.6396005325996 72.244263806387
22
- 108.73384179997886 134.47328134862394 3162.880454846513 215.45138754285665
23
- 238.49636899561344 2225.9561104691043 402.40727964384774 754.6792064294074
24
-
25
- GABPA_f1
1
+ > GABPA_f1
26
2
  615.2572649050138 697.0698715160123 1261.1903440712872 176.43506582414153
27
3
  996.4929869323321 805.1878697364007 693.7695793644275 254.5021102832924
28
4
  1106.9888035794224 508.19444415177276 1029.8329748714536 104.93632371380718
@@ -35,4 +11,28 @@ GABPA_f1
35
11
  202.05697400573305 28.799402471063658 2518.808687612104 0.2874822275405179
36
12
  172.92889618879767 521.1240363384483 106.38197600987633 1949.517637779338
37
13
  398.1679460365911 424.20938204069563 1706.4024212088275 221.17279703034018
38
- 764.2587933951809 675.0883944902433 1066.5413633225007 244.06399510852864
14
+ 764.2587933951809 675.0883944902433 1066.5413633225007 244.06399510852864
15
+ KLF4_f2
16
+ 1233.46088405354 93.18173277811673 1036.6014857092885 1258.2948629970272
17
+ 263.979242343185 5.314520555872139 3347.5949971525274 4.650205486388122
18
+ 76.7700780003465 6.643150694840173 3529.4896409394937 8.636095903292224
19
+ 57.86097393406657 18.102585643439472 3520.3342027139347 25.24120324653207
20
+ 518.1947904009378 1545.9062946905135 22.396758181071043 1535.0411222654507
21
+ 137.98151691820345 9.300410972776241 3456.320530770924 17.936506876068467
22
+ 115.27647661640499 81.51802997128804 1861.9425868567278 1562.801872093553
23
+ 227.8095486111286 42.84555258785854 3278.6396005325996 72.244263806387
24
+ 108.73384179997886 134.47328134862394 3162.880454846513 215.45138754285665
25
+ 238.49636899561344 2225.9561104691043 402.40727964384774 754.6792064294074
26
+
27
+ SP1_f1
28
+ 682.6436366358055 443.1455214015781 2075.655346294993 287.211468117951
29
+ 299.8883246804867 103.74338315843572 2613.8927022405364 471.1315623708902
30
+ 591.4892493324709 42.631827541794564 2845.1654083148564 9.36948726124641
31
+ 7.071084742361592 45.29093411231232 3432.8847704374107 3.409183158303573
32
+ 91.308984085713 19.1536481364332 3373.656949880137 4.5363903481026
33
+ 809.2082973387932 2246.941954176211 61.30766021687515 371.19806071846244
34
+ 120.56476435866055 42.4349244403591 3242.1560628684038 83.50022078295852
35
+ 13.72524477409959 35.858220519297525 3332.4066864946167 106.66582066236779
36
+ 558.1188080161639 90.0084504200356 2694.854973210736 145.67374080342415
37
+ 264.0088462230318 254.7175868081866 2796.88087480315 173.0486646159857
38
+ 519.46013914282 1874.9349086474765 654.5411208373813 439.7198038226514
data/test/test_helper.rb CHANGED
@@ -2,6 +2,7 @@ $lib_folder = File.dirname(__FILE__) + '/../lib'
2
2
  $LOAD_PATH.unshift $lib_folder
3
3
  require 'test/unit'
4
4
  require 'stringio'
5
+ require 'shellwords'
5
6
 
6
7
  require 'macroape/cli/find_threshold'
7
8
  require 'macroape/cli/find_pvalue'
@@ -47,25 +48,25 @@ module Helpers
47
48
  "ruby -I #{$lib_folder} #{$lib_folder}/../bin/#{executable} #{param_list}"
48
49
  end
49
50
  def self.find_threshold_output(param_list)
50
- capture_output{ Macroape::CLI::FindThreshold.main(param_list.split) }
51
+ capture_output{ Macroape::CLI::FindThreshold.main(param_list.shellsplit) }
51
52
  end
52
53
  def self.align_motifs_output(param_list)
53
- capture_output{ Macroape::CLI::AlignMotifs.main(param_list.split) }
54
+ capture_output{ Macroape::CLI::AlignMotifs.main(param_list.shellsplit) }
54
55
  end
55
56
  def self.find_pvalue_output(param_list)
56
- capture_output{ Macroape::CLI::FindPValue.main(param_list.split) }
57
+ capture_output{ Macroape::CLI::FindPValue.main(param_list.shellsplit) }
57
58
  end
58
59
  def self.eval_similarity_output(param_list)
59
- capture_output{ Macroape::CLI::EvalSimilarity.main(param_list.split) }
60
+ capture_output{ Macroape::CLI::EvalSimilarity.main(param_list.shellsplit) }
60
61
  end
61
62
  def self.eval_alignment_output(param_list)
62
- capture_output{ Macroape::CLI::EvalAlignment.main(param_list.split) }
63
+ capture_output{ Macroape::CLI::EvalAlignment.main(param_list.shellsplit) }
63
64
  end
64
65
  def self.scan_collection_output(param_list)
65
- capture_output{ Macroape::CLI::ScanCollection.main(param_list.split) }
66
+ capture_output{ Macroape::CLI::ScanCollection.main(param_list.shellsplit) }
66
67
  end
67
68
  def self.run_preprocess_collection(param_list)
68
- Macroape::CLI::PreprocessCollection.main(param_list.split)
69
+ Macroape::CLI::PreprocessCollection.main(param_list.shellsplit)
69
70
  end
70
71
 
71
72
  end
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: macroape
3
3
  version: !ruby/object:Gem::Version
4
- version: 3.3.5
4
+ version: 3.3.6
5
5
  prerelease:
6
6
  platform: ruby
7
7
  authors:
@@ -9,7 +9,7 @@ authors:
9
9
  autorequire:
10
10
  bindir: bin
11
11
  cert_chain: []
12
- date: 2012-09-04 00:00:00.000000000 Z
12
+ date: 2012-09-11 00:00:00.000000000 Z
13
13
  dependencies:
14
14
  - !ruby/object:Gem::Dependency
15
15
  name: bioinform
@@ -18,7 +18,7 @@ dependencies:
18
18
  requirements:
19
19
  - - ! '>='
20
20
  - !ruby/object:Gem::Version
21
- version: 0.1.5
21
+ version: 0.1.7
22
22
  type: :runtime
23
23
  prerelease: false
24
24
  version_requirements: !ruby/object:Gem::Requirement
@@ -26,7 +26,7 @@ dependencies:
26
26
  requirements:
27
27
  - - ! '>='
28
28
  - !ruby/object:Gem::Version
29
- version: 0.1.5
29
+ version: 0.1.7
30
30
  description: Macroape is an abbreviation for MAtrix CompaRisOn by Approximate P-value
31
31
  Estimation. It's a bioinformatic tool for evaluating similarity measure and best
32
32
  alignment between a pair of Position Weight Matrices(PWM), finding thresholds by
@@ -69,7 +69,6 @@ files:
69
69
  - lib/macroape/cli/find_threshold.rb
70
70
  - lib/macroape/cli/preprocess_collection.rb
71
71
  - lib/macroape/cli/scan_collection.rb
72
- - lib/macroape/collection.rb
73
72
  - lib/macroape/counting.rb
74
73
  - lib/macroape/pwm_compare.rb
75
74
  - lib/macroape/pwm_compare_aligned.rb
data/lib/macroape/collection.rb DELETED
@@ -1,22 +0,0 @@
1
- module Macroape
2
- class Collection
3
- attr_reader :rough_discretization, :precise_discretization, :background, :pvalues, :pwms, :infos
4
- def initialize(rough_discretization, precise_discretization, background, pvalues)
5
- @rough_discretization, @precise_discretization, @background, @pvalues = rough_discretization, precise_discretization, background, pvalues
6
- @pwms={}
7
- @infos={}
8
- end
9
- def add_pwm(pwm,info)
10
- @pwms[pwm.name] = pwm
11
- @infos[pwm.name] = info
12
- end
13
- def ==(other)
14
- @rough_discretization == other.rough_discretization &&
15
- @precise_discretization == other.precise_discretization &&
16
- @background == other.background &&
17
- @pvalues == other.pvalues &&
18
- @pwms == other.pwms &&
19
- @infos == other.infos
20
- end
21
- end
22
- end