macroape 3.3.7 → 3.3.8

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 (46) hide show
  1. data/README.md +2 -2
  2. data/Rakefile.rb +6 -6
  3. data/TODO.txt +23 -3
  4. data/benchmark/similarity_benchmark.rb +18 -18
  5. data/lib/macroape/aligned_pair_intersection.rb +4 -4
  6. data/lib/macroape/cli/align_motifs.rb +34 -28
  7. data/lib/macroape/cli/eval_alignment.rb +73 -47
  8. data/lib/macroape/cli/eval_similarity.rb +65 -40
  9. data/lib/macroape/cli/find_pvalue.rb +30 -34
  10. data/lib/macroape/cli/find_threshold.rb +52 -41
  11. data/lib/macroape/cli/preprocess_collection.rb +68 -58
  12. data/lib/macroape/cli/scan_collection.rb +89 -73
  13. data/lib/macroape/cli.rb +184 -1
  14. data/lib/macroape/counting.rb +31 -5
  15. data/lib/macroape/pwm_compare.rb +8 -2
  16. data/lib/macroape/pwm_compare_aligned.rb +15 -10
  17. data/lib/macroape/version.rb +2 -1
  18. data/macroape.gemspec +2 -1
  19. data/spec/count_distribution_spec.rb +11 -11
  20. data/test/align_motifs_test.rb +16 -4
  21. data/test/data/{AHR_si.pat → AHR_si.pwm} +0 -0
  22. data/test/data/{KLF3_f1.pat → KLF3_f1.pwm} +0 -0
  23. data/test/data/{KLF4_f2.pat → KLF4_f2.pwm} +0 -0
  24. data/test/data/KLF4_f2_scan_results_all.txt +1 -2
  25. data/test/data/KLF4_f2_scan_results_default_cutoff.txt +1 -2
  26. data/test/data/KLF4_f2_scan_results_precise_mode.txt +1 -2
  27. data/test/data/KLF4_f2_scan_results_weak_threshold.txt +2 -0
  28. data/test/data/{SP1_f1.pat → SP1_f1.pwm} +0 -0
  29. data/test/data/{SP1_f1_revcomp.pat → SP1_f1_revcomp.pwm} +0 -0
  30. data/test/data/collection_pcm_without_thresholds.yaml +186 -183
  31. data/test/data/collection_without_thresholds.yaml +186 -183
  32. data/test/data/{medium_motif.pat → medium_motif.pwm} +0 -0
  33. data/test/data/{short_motif.pat → short_motif.pwm} +0 -0
  34. data/test/data/test_collection/{GABPA_f1.pat → GABPA_f1.pwm} +0 -0
  35. data/test/data/test_collection/{KLF4_f2.pat → KLF4_f2.pwm} +0 -0
  36. data/test/data/test_collection/{SP1_f1.pat → SP1_f1.pwm} +0 -0
  37. data/test/data/test_collection.yaml +179 -176
  38. data/test/data/test_collection_weak.yaml +214 -0
  39. data/test/eval_alignment_test.rb +97 -21
  40. data/test/eval_similarity_test.rb +104 -26
  41. data/test/find_pvalue_test.rb +22 -9
  42. data/test/find_threshold_test.rb +76 -25
  43. data/test/preprocess_collection_test.rb +16 -21
  44. data/test/scan_collection_test.rb +26 -14
  45. data/test/test_helper.rb +96 -12
  46. metadata +44 -24
data/spec/count_distribution_spec.rb CHANGED
@@ -6,46 +6,46 @@ describe Bioinform::PWM do
6
6
  let :matrix_second do [[1,2,3,4],[2,3,4,5]] end
7
7
  let :pwm_first do Bioinform::PWM.new(matrix_first) end
8
8
  let :pwm_second do Bioinform::PWM.new(matrix_second) end
9
-
9
+
10
10
  context '#count_distribution_after_threshold' do
11
-
11
+
12
12
  it 'should return hash of score => count for all scores >= threshold' do
13
13
  distribution_first = pwm_first.count_distribution_after_threshold(0)
14
14
  distribution_first.keys.should == Array.product(*matrix_first).map{|score_row| score_row.inject(&:+)}
15
15
  distribution_first.values.uniq.should == [1]
16
-
16
+
17
17
  distribution_second = pwm_second.count_distribution_after_threshold(0)
18
18
  distribution_second.should == { 3=>1, 4=>2, 5=>3, 6=>4, 7=>3, 8=>2, 9=>1 }
19
-
19
+
20
20
  distribution_second = pwm_second.count_distribution_after_threshold(5)
21
21
  distribution_second.should == { 5=>3, 6=>4, 7=>3, 8=>2, 9=>1 }
22
22
  end
23
-
23
+
24
24
  it 'should use existing precalculated hash @count_distribution if it exists' do
25
25
  pwm = pwm_second;
26
26
  pwm.instance_variable_set :@count_distribution, { 3=>10, 4=>20, 5=>30, 6=>40, 7=>30, 8=>20, 9=>10 }
27
-
27
+
28
28
  distribution_second = pwm.count_distribution_after_threshold(0)
29
29
  distribution_second.should == { 3=>10, 4=>20, 5=>30, 6=>40, 7=>30, 8=>20, 9=>10 }
30
-
30
+
31
31
  distribution_second = pwm.count_distribution_after_threshold(5)
32
32
  distribution_second.should == { 5=>30, 6=>40, 7=>30, 8=>20, 9=>10 }
33
33
  end
34
34
  end
35
-
35
+
36
36
  context '#count_distribution' do
37
37
  it 'should return hash of score => count for all available scores' do
38
38
  pwm_second.count_distribution.should == { 3=>1, 4=>2, 5=>3, 6=>4, 7=>3, 8=>2, 9=>1 }
39
39
  end
40
-
40
+
41
41
  it 'should cache calculation in @count_distribution' do
42
42
  pwm = pwm_second;
43
43
  pwm.instance_variable_set :@count_distribution, { 3=>10, 4=>20, 5=>30, 6=>40, 7=>30, 8=>20, 9=>10 }
44
44
  pwm.count_distribution.should == { 3=>10, 4=>20, 5=>30, 6=>40, 7=>30, 8=>20, 9=>10 }
45
-
45
+
46
46
  pwm.instance_variable_set :@count_distribution, nil
47
47
  pwm.count_distribution.should == { 3=>1, 4=>2, 5=>3, 6=>4, 7=>3, 8=>2, 9=>1 }
48
48
  end
49
49
  end
50
-
50
+
51
51
  end
data/test/align_motifs_test.rb CHANGED
@@ -1,12 +1,24 @@
1
1
  require_relative 'test_helper'
2
2
 
3
3
  class TestAlignmotifs < Test::Unit::TestCase
4
+ def setup
5
+ @start_dir = Dir.pwd
6
+ Dir.chdir File.join(File.dirname(__FILE__), 'data')
7
+ end
8
+ def teardown
9
+ Dir.chdir(@start_dir)
10
+ end
11
+
4
12
  def test_align_motifs
5
- assert_equal "test/data/KLF4_f2.pat\t0\tdirect\ntest/data/KLF3_f1.pat\t-4\tdirect\ntest/data/SP1_f1_revcomp.pat\t-1\trevcomp\n",
6
- Helpers.align_motifs_output('test/data/KLF4_f2.pat test/data/KLF3_f1.pat test/data/SP1_f1_revcomp.pat')
13
+ assert_equal [%w[KLF4_f2.pwm 0 direct],
14
+ %w[KLF3_f1.pwm -4 direct],
15
+ %w[SP1_f1_revcomp.pwm -1 revcomp]],
16
+ Helpers.align_motifs_output('KLF4_f2.pwm KLF3_f1.pwm SP1_f1_revcomp.pwm')
7
17
  end
8
18
  def test_align_pcm_motifs
9
- assert_equal "test/data/KLF4_f2.pcm\t0\tdirect\ntest/data/KLF3_f1.pcm\t-4\tdirect\ntest/data/SP1_f1_revcomp.pcm\t-1\trevcomp\n",
10
- Helpers.align_motifs_output('--pcm test/data/KLF4_f2.pcm test/data/KLF3_f1.pcm test/data/SP1_f1_revcomp.pcm')
19
+ assert_equal [%w[KLF4_f2.pcm 0 direct],
20
+ %w[KLF3_f1.pcm -4 direct],
21
+ %w[SP1_f1_revcomp.pcm -1 revcomp]],
22
+ Helpers.align_motifs_output('--pcm KLF4_f2.pcm KLF3_f1.pcm SP1_f1_revcomp.pcm')
11
23
  end
12
24
  end
data/test/data/{AHR_si.pat → AHR_si.pwm} RENAMED
File without changes
data/test/data/{KLF3_f1.pat → KLF3_f1.pwm} RENAMED
File without changes
data/test/data/{KLF4_f2.pat → KLF4_f2.pwm} RENAMED
File without changes
data/test/data/KLF4_f2_scan_results_all.txt CHANGED
@@ -1,4 +1,3 @@
1
- #pwm similarity shift overlap orientation
2
1
  KLF4_f2 1.0 0 10 direct
3
2
  SP1_f1 0.22754919499105544 -1 10 direct
4
- GABPA_f1 0.00043527658136684877 -8 5 direct
3
+ GABPA_f1 0.00043527658136684877 -8 5 direct
data/test/data/KLF4_f2_scan_results_default_cutoff.txt CHANGED
@@ -1,3 +1,2 @@
1
- #pwm similarity shift overlap orientation
2
1
  KLF4_f2 1.0 0 10 direct
3
- SP1_f1 0.22754919499105544 -1 10 direct
2
+ SP1_f1 0.22754919499105544 -1 10 direct
data/test/data/KLF4_f2_scan_results_precise_mode.txt CHANGED
@@ -1,4 +1,3 @@
1
- #pwm similarity shift overlap orientation
2
1
  KLF4_f2 1.0 0 10 direct *
3
2
  SP1_f1 0.2420758234928527 -1 10 direct *
4
- GABPA_f1 0.00043527658136684877 -8 5 direct
3
+ GABPA_f1 0.00043527658136684877 -8 5 direct .
data/test/data/KLF4_f2_scan_results_weak_threshold.txt ADDED
@@ -0,0 +1,2 @@
1
+ KLF4_f2 1.0 0 10 direct
2
+ SP1_f1 0.2580456407255705 -1 10 direct
data/test/data/{SP1_f1.pat → SP1_f1.pwm} RENAMED
File without changes
data/test/data/collection_pcm_without_thresholds.yaml CHANGED
@@ -1,185 +1,188 @@
1
- --- &18345276 !ruby/object:Bioinform::Collection
2
- collection:
3
- - - !ruby/object:Bioinform::PCM
4
- parameters: !ruby/object:OpenStruct
5
- table:
6
- :name: GABPA_f1
7
- :tags:
8
- - *18345276
9
- :background:
10
- - 1
11
- - 1
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- - 1
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- - 1
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- modifiable: true
15
- matrix:
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- - - 615.2572649050138
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- - 697.0698715160123
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- - 1261.1903440712872
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- - 176.43506582414153
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- - - 996.4929869323321
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- - 254.5021102832924
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- - - 1106.9888035794224
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- - 1029.8329748714536
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- - - 143.7121486195701
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- - - 362.9541452731307
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- - - 2748.2567506938462
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- - 0.0
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- - - 2726.6484322711017
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- - 21.00425622500253
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- - - 172.92889618879767
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- - !ruby/object:OpenStruct
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- table: {}
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- - - !ruby/object:Bioinform::PCM
71
- parameters: !ruby/object:OpenStruct
72
- table:
73
- :name: KLF4_f2
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- :tags:
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- - *18345276
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- :background:
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- - 1
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- - 1
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- - 1
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- - 1
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- modifiable: true
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- matrix:
83
- - - 1233.46088405354
84
- - 93.18173277811673
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- - 1036.6014857092885
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- - 1258.2948629970272
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- - - 263.979242343185
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- - - 518.1947904009378
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- - 1545.9062946905135
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- - - 137.98151691820345
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- - 9.300410972776241
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- - 17.936506876068467
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- - - 115.27647661640499
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- - 81.51802997128804
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- - 1861.9425868567278
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- - 1562.801872093553
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- - - 227.8095486111286
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- - 42.84555258785854
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- - 3278.6396005325996
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- - - 108.73384179997886
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- - - 238.49636899561344
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- - 2225.9561104691043
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- - 402.40727964384774
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- - 754.6792064294074
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- - !ruby/object:OpenStruct
124
- table: {}
125
- - - !ruby/object:Bioinform::PCM
126
- parameters: !ruby/object:OpenStruct
127
- table:
128
- :name: SP1_f1
129
- :tags:
130
- - *18345276
131
- :background:
132
- - 1
133
- - 1
134
- - 1
135
- - 1
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- modifiable: true
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- matrix:
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- - - 682.6436366358055
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- - 443.1455214015781
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- - 2075.655346294993
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- - 287.211468117951
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- - - 13.72524477409959
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- - 3332.4066864946167
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- - - 558.1188080161639
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- - 654.5411208373813
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- - 439.7198038226514
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- - !ruby/object:OpenStruct
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- table: {}
1
+ --- !ruby/object:Bioinform::Collection
2
+ container:
3
+ - !ruby/object:Bioinform::Motif
4
+ parameters: !ruby/object:OpenStruct
5
+ table:
6
+ :original_data_model: :pcm
7
+ :pcm: !ruby/object:Bioinform::PCM
8
+ parameters: !ruby/object:OpenStruct
9
+ table:
10
+ :name: GABPA_f1
11
+ :background:
12
+ - 1
13
+ - 1
14
+ - 1
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+ - 1
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+ modifiable: true
17
+ matrix:
18
+ - - 615.2572649050138
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21
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22
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+ - 1066.5413633225007
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+ - 244.06399510852864
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+ modifiable: true
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+ - !ruby/object:Bioinform::Motif
72
+ parameters: !ruby/object:OpenStruct
73
+ table:
74
+ :original_data_model: :pcm
75
+ :pcm: !ruby/object:Bioinform::PCM
76
+ parameters: !ruby/object:OpenStruct
77
+ table:
78
+ :name: KLF4_f2
79
+ :background:
80
+ - 1
81
+ - 1
82
+ - 1
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+ - 1
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+ modifiable: true
85
+ matrix:
86
+ - - 1233.46088405354
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+ - 93.18173277811673
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+ - 1036.6014857092885
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+ - 1258.2948629970272
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+ modifiable: true
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+ - !ruby/object:Bioinform::Motif
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+ parameters: !ruby/object:OpenStruct
129
+ table:
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+ :original_data_model: :pcm
131
+ :pcm: !ruby/object:Bioinform::PCM
132
+ parameters: !ruby/object:OpenStruct
133
+ table:
134
+ :name: SP1_f1
135
+ :background:
136
+ - 1
137
+ - 1
138
+ - 1
139
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+ modifiable: true
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+ matrix:
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+ modifiable: true
184
187
  parameters: !ruby/object:OpenStruct
185
188
  table: {}