macroape 3.3.5 → 3.3.6

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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