bioinform 0.1.7 → 0.1.8

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Files changed (73) hide show
  1. data/TODO.txt +7 -2
  2. data/bin/merge_into_collection +4 -0
  3. data/bin/pcm2pwm +1 -1
  4. data/bin/split_motifs +1 -1
  5. data/bioinform.gemspec +2 -0
  6. data/lib/bioinform/cli/merge_into_collection.rb +76 -0
  7. data/lib/bioinform/cli/pcm2pwm.rb +20 -20
  8. data/lib/bioinform/cli/split_motifs.rb +21 -20
  9. data/lib/bioinform/cli.rb +16 -2
  10. data/lib/bioinform/data_models/collection.rb +13 -10
  11. data/lib/bioinform/data_models/pcm.rb +2 -2
  12. data/lib/bioinform/data_models/pm.rb +24 -37
  13. data/lib/bioinform/data_models/ppm.rb +2 -2
  14. data/lib/bioinform/data_models/pwm.rb +2 -2
  15. data/lib/bioinform/data_models.rb +8 -8
  16. data/lib/bioinform/parsers/parser.rb +10 -5
  17. data/lib/bioinform/parsers/splittable_parser.rb +57 -0
  18. data/lib/bioinform/parsers/string_fantom_parser.rb +3 -3
  19. data/lib/bioinform/parsers/string_parser.rb +5 -24
  20. data/lib/bioinform/parsers/trivial_parser.rb +19 -3
  21. data/lib/bioinform/parsers/yaml_parser.rb +35 -0
  22. data/lib/bioinform/parsers.rb +6 -4
  23. data/lib/bioinform/support/parameters.rb +19 -0
  24. data/lib/bioinform/support/partial_sums.rb +1 -1
  25. data/lib/bioinform/support.rb +11 -10
  26. data/lib/bioinform/version.rb +1 -1
  27. data/lib/bioinform.rb +5 -5
  28. data/spec/cli/cli_spec.rb +8 -7
  29. data/spec/cli/data/merge_into_collection/GABPA_f1.pwm +14 -0
  30. data/spec/cli/data/{KLF4_f2.pwm.result → merge_into_collection/KLF4_f2.pwm} +0 -0
  31. data/spec/cli/data/{SP1_f1.pwm.result → merge_into_collection/SP1_f1.pwm} +0 -0
  32. data/spec/cli/data/merge_into_collection/collection.txt.result +40 -0
  33. data/spec/cli/data/merge_into_collection/collection.yaml.result +185 -0
  34. data/spec/cli/data/merge_into_collection/collection_pwm.yaml.result +185 -0
  35. data/spec/cli/data/merge_into_collection/pwm_folder/GABPA_f1.pwm +14 -0
  36. data/spec/cli/data/merge_into_collection/pwm_folder/KLF4_f2.pwm +11 -0
  37. data/spec/cli/data/merge_into_collection/pwm_folder/SP1_f1.pwm +12 -0
  38. data/spec/cli/data/{KLF4 f2 spaced name.pcm → pcm2pwm/KLF4 f2 spaced name.pcm} +0 -0
  39. data/spec/cli/data/{KLF4_f2.pcm → pcm2pwm/KLF4_f2.pcm} +0 -0
  40. data/spec/cli/data/pcm2pwm/KLF4_f2.pwm.result +11 -0
  41. data/spec/cli/data/{SP1_f1.pcm → pcm2pwm/SP1_f1.pcm} +0 -0
  42. data/spec/cli/data/pcm2pwm/SP1_f1.pwm.result +12 -0
  43. data/spec/cli/data/split_motifs/GABPA_f1.mat.result +14 -0
  44. data/spec/cli/data/split_motifs/KLF4_f2.mat.result +11 -0
  45. data/spec/cli/data/split_motifs/SP1_f1.mat.result +12 -0
  46. data/spec/cli/data/split_motifs/collection.yaml +197 -0
  47. data/spec/cli/data/split_motifs/plain_collection.txt +38 -0
  48. data/spec/cli/merge_into_collection_spec.rb +100 -0
  49. data/spec/cli/pcm2pwm_spec.rb +3 -3
  50. data/spec/cli/split_motifs_spec.rb +74 -3
  51. data/spec/data_models/collection_spec.rb +2 -2
  52. data/spec/data_models/pcm_spec.rb +2 -2
  53. data/spec/data_models/pm_spec.rb +10 -27
  54. data/spec/data_models/ppm_spec.rb +2 -2
  55. data/spec/data_models/pwm_spec.rb +3 -3
  56. data/spec/fabricators/collection_fabricator.rb +8 -0
  57. data/spec/fabricators/pm_fabricator.rb +43 -0
  58. data/spec/parsers/parser_spec.rb +29 -37
  59. data/spec/parsers/string_fantom_parser_spec.rb +38 -35
  60. data/spec/parsers/string_parser_spec.rb +33 -66
  61. data/spec/parsers/trivial_parser_spec.rb +48 -6
  62. data/spec/parsers/yaml_parser_spec.rb +50 -0
  63. data/spec/spec_helper.rb +2 -6
  64. data/spec/support/advanced_scan_spec.rb +2 -2
  65. data/spec/support/array_product_spec.rb +2 -2
  66. data/spec/support/array_zip_spec.rb +2 -2
  67. data/spec/support/collect_hash_spec.rb +2 -2
  68. data/spec/support/delete_many_spec.rb +2 -2
  69. data/spec/support/inverf_spec.rb +2 -2
  70. data/spec/support/multiline_squish_spec.rb +2 -2
  71. data/spec/support/partial_sums_spec.rb +2 -2
  72. data/spec/support/same_by_spec.rb +2 -2
  73. metadata +86 -12
data/lib/bioinform/parsers/trivial_parser.rb CHANGED
@@ -1,5 +1,7 @@
1
- require 'bioinform/support'
2
- require 'bioinform/parsers/parser'
1
+ require_relative '../support'
2
+ require_relative '../parsers/parser'
3
+ require_relative '../data_models/collection'
4
+ require 'yaml'
3
5
 
4
6
  module Bioinform
5
7
  # TrivialParser can be used to parse hashes returned by #parse method of other parsers:
@@ -11,7 +13,21 @@ module Bioinform
11
13
  @input = input
12
14
  end
13
15
  def parse!
14
- input
16
+ case input
17
+ when PM then input
18
+ when OpenStruct then input
19
+ when Hash then OpenStruct.new(input)
20
+ end
21
+ end
22
+ end
23
+
24
+ class TrivialCollectionParser < Parser
25
+ include MultipleMotifsParser
26
+ def initialize(input)
27
+ @input = input
28
+ end
29
+ def parse!
30
+ input.collection.shift.first
15
31
  end
16
32
  end
17
33
  end
data/lib/bioinform/parsers/yaml_parser.rb ADDED
@@ -0,0 +1,35 @@
1
+ require_relative '../support'
2
+ require_relative 'parser'
3
+ require_relative '../data_models/collection'
4
+ require 'yaml'
5
+
6
+ module Bioinform
7
+ # YAMLParser can be used to parse hashes returned by #parse method of other parsers:
8
+ # yaml_dump_of_pm = PM.new(...).to_yaml
9
+ # PM.new(yaml_dump_of_pm, YAMLParser)
10
+ class YAMLParser < Parser
11
+ def initialize(input)
12
+ @input = input
13
+ end
14
+ def parse!
15
+ YAML.load(input)
16
+ rescue Psych::SyntaxError
17
+ raise 'parsing error'
18
+ end
19
+ end
20
+
21
+ class YAMLCollectionParser < Parser
22
+ include MultipleMotifsParser
23
+ def initialize(input)
24
+ @input = input
25
+ end
26
+ def collection
27
+ @collection ||= YAML.load(input)
28
+ end
29
+ def parse!
30
+ collection.collection.shift.first
31
+ rescue Psych::SyntaxError
32
+ raise 'parsing error'
33
+ end
34
+ end
35
+ end
data/lib/bioinform/parsers.rb CHANGED
@@ -1,4 +1,6 @@
1
- require 'bioinform/parsers/parser'
2
- require 'bioinform/parsers/trivial_parser'
3
- require 'bioinform/parsers/string_parser'
4
- require 'bioinform/parsers/string_fantom_parser'
1
+ require_relative 'parsers/parser'
2
+ require_relative 'parsers/trivial_parser'
3
+ require_relative 'parsers/yaml_parser'
4
+ require_relative 'parsers/string_parser'
5
+ require_relative 'parsers/string_fantom_parser'
6
+ require_relative 'parsers/splittable_parser'
data/lib/bioinform/support/parameters.rb ADDED
@@ -0,0 +1,19 @@
1
+ require 'ostruct'
2
+ module Parameters
3
+ def self.included(base)
4
+ base.extend(ClassMethods)
5
+ end
6
+ module ClassMethods
7
+ def make_parameters(*params)
8
+ params.each do |param|
9
+ define_method(param){ parameters.send(param) }
10
+ define_method("#{param}="){|new_value| parameters.send("#{param}=", new_value) }
11
+ end
12
+ end
13
+ end
14
+ def parameters; @parameters ||= OpenStruct.new; end
15
+ def set_parameters(hsh)
16
+ hsh.each{|k,v| send("#{k}=", v) }
17
+ self
18
+ end
19
+ end
data/lib/bioinform/support/partial_sums.rb CHANGED
@@ -1,4 +1,4 @@
1
- require 'bioinform/support/collect_hash'
1
+ require_relative 'collect_hash'
2
2
 
3
3
  class Array
4
4
  def partial_sums(initial = 0.0)
data/lib/bioinform/support.rb CHANGED
@@ -1,16 +1,17 @@
1
1
  require 'active_support/core_ext/string/filters'
2
2
  require 'active_support/core_ext/hash/indifferent_access'
3
3
 
4
- require 'bioinform/support/collect_hash'
5
- require 'bioinform/support/delete_many'
6
- require 'bioinform/support/multiline_squish'
7
- require 'bioinform/support/same_by'
8
- require 'bioinform/support/inverf'
9
- require 'bioinform/support/deep_dup'
4
+ require_relative 'support/collect_hash'
5
+ require_relative 'support/delete_many'
6
+ require_relative 'support/multiline_squish'
7
+ require_relative 'support/same_by'
8
+ require_relative 'support/inverf'
9
+ require_relative 'support/deep_dup'
10
10
 
11
- require 'bioinform/support/partial_sums'
11
+ require_relative 'support/partial_sums'
12
12
 
13
- require 'bioinform/support/array_zip'
14
- require 'bioinform/support/array_product'
13
+ require_relative 'support/array_zip'
14
+ require_relative 'support/array_product'
15
15
 
16
- require 'bioinform/support/advanced_scan'
16
+ require_relative 'support/advanced_scan'
17
+ require_relative 'support/parameters'
data/lib/bioinform/version.rb CHANGED
@@ -1,3 +1,3 @@
1
1
  module Bioinform
2
- VERSION = "0.1.7"
2
+ VERSION = "0.1.8"
3
3
  end
data/lib/bioinform.rb CHANGED
@@ -1,8 +1,8 @@
1
- require 'bioinform/version'
2
- require 'bioinform/support'
3
- require 'bioinform/parsers'
4
- require 'bioinform/data_models'
5
- require 'bioinform/cli'
1
+ require_relative 'bioinform/version'
2
+ require_relative 'bioinform/support'
3
+ require_relative 'bioinform/parsers'
4
+ require_relative 'bioinform/data_models'
5
+ require_relative 'bioinform/cli'
6
6
 
7
7
  module Bioinform
8
8
  # Your code goes here...
data/spec/cli/cli_spec.rb CHANGED
@@ -1,13 +1,14 @@
1
- require 'spec_helper'
2
- require 'bioinform/cli'
1
+ require_relative '../spec_helper'
2
+ require_relative '../../lib/bioinform/cli'
3
3
 
4
4
  describe Bioinform::CLI do
5
- describe '::output_filename' do
5
+ describe '.change_folder_and_extension' do
6
6
  it 'should change extension and folder' do
7
- Bioinform::CLI.output_filename('test.pcm', 'pwm', '.').should == './test.pwm'
8
- Bioinform::CLI.output_filename('test.pcm', 'pat', 'pwm_folder').should == 'pwm_folder/test.pat'
9
- Bioinform::CLI.output_filename('pcm/test.pcm', 'pat', 'pwm_folder').should == 'pwm_folder/test.pat'
10
- Bioinform::CLI.output_filename('test.pcm', 'pat', '../pwm_folder').should == '../pwm_folder/test.pat'
7
+ extend Bioinform::CLI::Helpers
8
+ change_folder_and_extension('test.pcm', 'pwm', '.').should == './test.pwm'
9
+ change_folder_and_extension('test.pcm', 'pat', 'pwm_folder').should == 'pwm_folder/test.pat'
10
+ change_folder_and_extension('pcm/test.pcm', 'pat', 'pwm_folder').should == 'pwm_folder/test.pat'
11
+ change_folder_and_extension('test.pcm', 'pat', '../pwm_folder').should == '../pwm_folder/test.pat'
11
12
  end
12
13
  end
13
14
  end
data/spec/cli/data/merge_into_collection/GABPA_f1.pwm ADDED
@@ -0,0 +1,14 @@
1
+ GABPA_f1
2
+ -0.1106670158341858 0.013801606113892391 0.6054596108973699 -1.3518085041421573
3
+ 0.37030668921643345 0.15761121480429963 0.009069314183831202 -0.9888619717703562
4
+ 0.47526546359546684 -0.3011678534572083 0.4031522994412777 -1.8638752827041059
5
+ -1.5544255540164373 1.1082369687811506 -0.2814091552834454 -5.30708531823271
6
+ -0.6362037835776368 1.235338189985594 -3.5801322928552253 -5.717323067092849
7
+ -5.852906870733575 -5.852906870733575 1.3841383838057746 -5.852906870733575
8
+ -5.852906870733575 -5.852906870733575 1.3841383838057746 -5.852906870733575
9
+ 1.3835219739184708 -5.2341956006430985 -5.852906870733575 -5.852906870733575
10
+ 1.3756340514956562 -5.394962755562375 -5.394962755562375 -3.401117964959733
11
+ -1.2176198315414444 -3.109079898175411 1.2964067931472216 -5.717323067092849
12
+ -1.3716559438167257 -0.2761401935045069 -1.8504445165866068 1.0404320473626856
13
+ -0.5440863133031895 -0.48103682561971345 0.907381908447086 -1.1280642594012078
14
+ 0.10557340209290218 -0.01814819455289191 0.4381106695354074 -1.0304105539540915
data/spec/cli/data/merge_into_collection/collection.txt.result ADDED
@@ -0,0 +1,40 @@
1
+ GABPA_f1
2
+ -0.1106670158341858 0.013801606113892391 0.6054596108973699 -1.3518085041421573
3
+ 0.37030668921643345 0.15761121480429963 0.009069314183831202 -0.9888619717703562
4
+ 0.47526546359546684 -0.3011678534572083 0.4031522994412777 -1.8638752827041059
5
+ -1.5544255540164373 1.1082369687811506 -0.2814091552834454 -5.30708531823271
6
+ -0.6362037835776368 1.235338189985594 -3.5801322928552253 -5.717323067092849
7
+ -5.852906870733575 -5.852906870733575 1.3841383838057746 -5.852906870733575
8
+ -5.852906870733575 -5.852906870733575 1.3841383838057746 -5.852906870733575
9
+ 1.3835219739184708 -5.2341956006430985 -5.852906870733575 -5.852906870733575
10
+ 1.3756340514956562 -5.394962755562375 -5.394962755562375 -3.401117964959733
11
+ -1.2176198315414444 -3.109079898175411 1.2964067931472216 -5.717323067092849
12
+ -1.3716559438167257 -0.2761401935045069 -1.8504445165866068 1.0404320473626856
13
+ -0.5440863133031895 -0.48103682561971345 0.907381908447086 -1.1280642594012078
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
+
28
+ SP1_f1
29
+ -0.24435707885585292 -0.674823404693731 0.8657012535789866 -1.1060188862599287
30
+ -1.0631255752097797 -2.111925969423868 1.0960627561110403 -0.6138563775211977
31
+ -0.3872276234760535 -2.9739851913218045 1.1807800242010378 -4.338927525031566
32
+ -4.563896055436894 -2.9161633002532277 1.3684371349982638 -5.077972423609655
33
+ -2.2369752892820083 -3.7196436313301846 1.3510439136452734 -4.889930670508233
34
+ -0.07473964149330865 0.944919654762011 -2.6246857648086044 -0.8510983487822436
35
+ -1.9643526491643322 -2.978402770880115 1.3113096718240573 -2.324334259499025
36
+ -4.0155484139655835 -3.1384268078096667 1.3387488589788057 -2.084673903537648
37
+ -0.44509385828355363 -2.2510053061629702 1.1265431574368685 -1.7780413702431372
38
+ -1.1896356092245048 -1.2251832285630027 1.1636760063747527 -1.6080243648157353
39
+ -0.5166047365590571 0.7641033353626657 -0.2862677570028208 -0.68254820978656
40
+
data/spec/cli/data/merge_into_collection/collection.yaml.result ADDED
@@ -0,0 +1,185 @@
1
+ --- &19257216 !ruby/object:Bioinform::Collection
2
+ collection:
3
+ - - !ruby/object:Bioinform::PM
4
+ parameters: !ruby/object:OpenStruct
5
+ table:
6
+ :name: GABPA_f1
7
+ :tags:
8
+ - *19257216
9
+ :background:
10
+ - 1
11
+ - 1
12
+ - 1
13
+ - 1
14
+ modifiable: true
15
+ matrix:
16
+ - - -0.1106670158341858
17
+ - 0.013801606113892391
18
+ - 0.6054596108973699
19
+ - -1.3518085041421573
20
+ - - 0.37030668921643345
21
+ - 0.15761121480429963
22
+ - 0.009069314183831202
23
+ - -0.9888619717703562
24
+ - - 0.47526546359546684
25
+ - -0.3011678534572083
26
+ - 0.4031522994412777
27
+ - -1.8638752827041059
28
+ - - -1.5544255540164373
29
+ - 1.1082369687811506
30
+ - -0.2814091552834454
31
+ - -5.30708531823271
32
+ - - -0.6362037835776368
33
+ - 1.235338189985594
34
+ - -3.5801322928552253
35
+ - -5.717323067092849
36
+ - - -5.852906870733575
37
+ - -5.852906870733575
38
+ - 1.3841383838057746
39
+ - -5.852906870733575
40
+ - - -5.852906870733575
41
+ - -5.852906870733575
42
+ - 1.3841383838057746
43
+ - -5.852906870733575
44
+ - - 1.3835219739184708
45
+ - -5.2341956006430985
46
+ - -5.852906870733575
47
+ - -5.852906870733575
48
+ - - 1.3756340514956562
49
+ - -5.394962755562375
50
+ - -5.394962755562375
51
+ - -3.401117964959733
52
+ - - -1.2176198315414444
53
+ - -3.109079898175411
54
+ - 1.2964067931472216
55
+ - -5.717323067092849
56
+ - - -1.3716559438167257
57
+ - -0.2761401935045069
58
+ - -1.8504445165866068
59
+ - 1.0404320473626856
60
+ - - -0.5440863133031895
61
+ - -0.48103682561971345
62
+ - 0.907381908447086
63
+ - -1.1280642594012078
64
+ - - 0.10557340209290218
65
+ - -0.01814819455289191
66
+ - 0.4381106695354074
67
+ - -1.0304105539540915
68
+ - !ruby/object:OpenStruct
69
+ table: {}
70
+ - - !ruby/object:Bioinform::PM
71
+ parameters: !ruby/object:OpenStruct
72
+ table:
73
+ :name: KLF4_f2
74
+ :tags:
75
+ - *19257216
76
+ :background:
77
+ - 1
78
+ - 1
79
+ - 1
80
+ - 1
81
+ modifiable: true
82
+ matrix:
83
+ - - 0.30861857265872605
84
+ - -2.254321000121579
85
+ - 0.13505703522674192
86
+ - 0.3285194224375633
87
+ - - -1.227018967707036
88
+ - -4.814127713368663
89
+ - 1.3059890687390967
90
+ - -4.908681463544344
91
+ - - -2.443469374521196
92
+ - -4.648238485031404
93
+ - 1.3588686548279805
94
+ - -4.441801801188402
95
+ - - -2.7177827948276123
96
+ - -3.8073538975356565
97
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data/spec/cli/data/merge_into_collection/pwm_folder/GABPA_f1.pwm ADDED
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data/spec/cli/data/merge_into_collection/pwm_folder/KLF4_f2.pwm ADDED
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data/spec/cli/data/merge_into_collection/pwm_folder/SP1_f1.pwm ADDED
@@ -0,0 +1,12 @@
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data/spec/cli/data/{KLF4_f2.pcm → pcm2pwm/KLF4_f2.pcm} RENAMED
File without changes
data/spec/cli/data/pcm2pwm/KLF4_f2.pwm.result ADDED
@@ -0,0 +1,11 @@
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data/spec/cli/data/{SP1_f1.pcm → pcm2pwm/SP1_f1.pcm} RENAMED
File without changes