bioinform 0.1.7 → 0.1.8

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 (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
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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