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.
- data/lib/macroape.rb +0 -1
- data/lib/macroape/cli/preprocess_collection.rb +9 -6
- data/lib/macroape/cli/scan_collection.rb +14 -17
- data/lib/macroape/version.rb +1 -1
- data/macroape.gemspec +2 -2
- data/test/data/test_collection.yaml +57 -47
- data/test/data/test_collection_single_file.txt +25 -25
- data/test/data/test_collection_single_file_pcm.txt +26 -26
- data/test/test_helper.rb +8 -7
- metadata +4 -5
- data/lib/macroape/collection.rb +0 -22
data/lib/macroape.rb
CHANGED
@@ -71,10 +71,13 @@ module Macroape
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end
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pvalues = default_pvalues if pvalues.empty?
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-
collection =
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collection = Bioinform::Collection.new(rough_discretization: rough_discretization,
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precise_discretization: precise_discretization,
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background: background,
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pvalues: pvalues)
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if File.directory?(data_source)
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motifs = Dir.glob(File.join(data_source,'*')).map do |filename|
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motifs = Dir.glob(File.join(data_source,'*')).sort.map do |filename|
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pwm = data_model.new(File.read(filename))
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pwm.name ||= File.basename(filename, File.extname(filename))
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pwm
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@@ -98,18 +101,18 @@ module Macroape
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# Otherwise it should skip motif and tell you about this
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# Also two command line options to fail on skipping or to skip silently should be included
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info =
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info = OpenStruct.new(rough: {}, precise: {})
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pwm.background!(background).max_hash_size!(max_hash_size)
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pwm.discrete(rough_discretization).thresholds(*pvalues) do |pvalue, threshold, real_pvalue|
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info
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info.rough[pvalue] = threshold / rough_discretization
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end
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pwm.discrete(precise_discretization).thresholds(*pvalues) do |pvalue, threshold, real_pvalue|
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info
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info.precise[pvalue] = threshold / precise_discretization
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end
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-
collection.
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collection.add_pm(pwm, info)
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end
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File.open(output_file,'w') do |f|
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f.puts(collection.to_yaml)
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@@ -46,7 +46,7 @@ module Macroape
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pvalue = 0.0005
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cutoff = 0.05 # minimal similarity to output
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collection = YAML.load_file(collection_file)
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-
background_query = collection.background
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+
background_query = collection.parameters.background
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max_hash_size = 1000000
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max_pair_hash_size = 1000
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@@ -80,7 +80,7 @@ module Macroape
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end
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end
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-
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
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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
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if filename == '.stdin'
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query_input = $stdin.read
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@@ -92,8 +92,8 @@ module Macroape
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query_pwm = data_model.new(query_input).to_pwm
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query_pwm.background(background_query).max_hash_size(max_hash_size)
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query_pwm_rough = query_pwm.discrete(collection.rough_discretization)
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query_pwm_precise = query_pwm.discrete(collection.precise_discretization)
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query_pwm_rough = query_pwm.discrete(collection.parameters.rough_discretization)
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query_pwm_precise = query_pwm.discrete(collection.parameters.precise_discretization)
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query_threshold_rough = query_pwm_rough.threshold(pvalue)
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query_threshold_precise = query_pwm_precise.threshold(pvalue)
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@@ -101,19 +101,16 @@ module Macroape
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similarities = {}
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precision_file_mode = {}
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collection.
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-
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pwm.background(collection.background).max_hash_size(max_hash_size)
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pwm_rough = pwm.discrete(collection.rough_discretization)
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pwm_precise = pwm.discrete(collection.precise_discretization)
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-
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STDERR.puts pwm.name unless silent
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collection.each do |pwm, pwm_info|
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name = pwm.name
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pwm.background(collection.parameters.background).max_hash_size(max_hash_size)
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pwm_rough = pwm.discrete(collection.parameters.rough_discretization)
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pwm_precise = pwm.discrete(collection.parameters.precise_discretization)
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pwm_threshold_rough = pwm_info.rough[pvalue] * collection.parameters.rough_discretization
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pwm_threshold_precise = pwm_info.precise[pvalue] * collection.parameters.precise_discretization
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STDERR.puts name unless silent
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cmp = Macroape::PWMCompare.new(query_pwm_rough, pwm_rough).max_hash_size(max_pair_hash_size)
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info = cmp.jaccard(query_threshold_rough, pwm_threshold_rough)
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precision_file_mode[name] = :rough
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data/lib/macroape/version.rb
CHANGED
data/macroape.gemspec
CHANGED
@@ -8,12 +8,12 @@ Gem::Specification.new do |gem|
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gem.summary = %q{PWM comparison tool using MACROAPE approach}
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gem.homepage = "http://autosome.ru/macroape/"
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-
gem.files = `git ls-files`.split(
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gem.files = `git ls-files`.split($/)
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gem.executables = gem.files.grep(%r{^bin/}).map{ |f| File.basename(f) }
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gem.test_files = gem.files.grep(%r{^(test|spec|features)/})
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gem.name = "macroape"
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gem.require_paths = ["lib"]
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gem.version = Macroape::VERSION
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gem.add_dependency('bioinform', '>= 0.1.
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gem.add_dependency('bioinform', '>= 0.1.7')
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end
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@@ -1,17 +1,6 @@
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--- !ruby/object:
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- 0.0001
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- 5.0e-05
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background: &17959680
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- 1
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- 1
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- 1
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- 1
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precise_discretization: 10
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rough_discretization: 1
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pwms:
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GABPA_f1: !ruby/object:Bioinform::PWM
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--- &18156900 !ruby/object:Bioinform::Collection
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collection:
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- - !ruby/object:Bioinform::PWM
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matrix:
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- - -0.1106670158341858
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- 0.013801606113892391
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@@ -66,9 +55,25 @@ pwms:
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- 0.4381106695354074
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- -1.0304105539540915
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name: GABPA_f1
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tags:
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- *18156900
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background: &18124572
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- 1
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- 1
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- 1
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- 1
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max_hash_size: 1000000
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- !ruby/object:OpenStruct
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table:
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:rough:
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5.0e-05: 16.1
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0.0001: 15.1
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0.0005: 12.1
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:precise:
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5.0e-05: 8.61
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0.0001: 7.609999999999999
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0.0005: 4.51
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- - !ruby/object:Bioinform::PWM
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matrix:
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- - 0.30861857265872605
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- -2.254321000121579
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@@ -111,9 +116,21 @@ pwms:
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- -0.8080773665408135
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name: KLF4_f2
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tags:
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- *18156900
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background: *18124572
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max_hash_size: 1000000
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- !ruby/object:OpenStruct
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table:
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:rough:
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5.0e-05: 14.1
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0.0001: 13.1
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0.0005: 11.1
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:precise:
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5.0e-05: 8.51
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0.0001: 7.909999999999999
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0.0005: 5.8100000000000005
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- - !ruby/object:Bioinform::PWM
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matrix:
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- - -0.24435707885585292
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@@ -160,33 +177,26 @@ pwms:
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name: SP1_f1
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tags:
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- *18156900
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background: *18124572
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max_hash_size: 1000000
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:
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SP1_f1:
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:rough:
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:precise:
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0.0001: 7.709999999999999
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0.0005: 5.61
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- !ruby/object:OpenStruct
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table:
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:rough:
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0.0001: 14.1
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0.0005: 11.1
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:precise:
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5.0e-05: 8.51
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0.0001: 7.709999999999999
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0.0005: 5.61
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parameters: !ruby/object:OpenStruct
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table:
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:rough_discretization: 1
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:precise_discretization: 10
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:background: *18124572
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:pvalues:
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- 0.0005
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- 0.0001
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- 5.0e-05
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@@ -1,28 +1,4 @@
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>
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-0.24435707885585292 -0.674823404693731 0.8657012535789866 -1.1060188862599287
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-1.0631255752097797 -2.111925969423868 1.0960627561110403 -0.6138563775211977
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-0.3872276234760535 -2.9739851913218045 1.1807800242010378 -4.338927525031566
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-4.563896055436894 -2.9161633002532277 1.3684371349982638 -5.077972423609655
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-2.2369752892820083 -3.7196436313301846 1.3510439136452734 -4.889930670508233
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-0.07473964149330865 0.944919654762011 -2.6246857648086044 -0.8510983487822436
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-1.9643526491643322 -2.978402770880115 1.3113096718240573 -2.324334259499025
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-0.44509385828355363 -2.2510053061629702 1.1265431574368685 -1.7780413702431372
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-1.1896356092245048 -1.2251832285630027 1.1636760063747527 -1.6080243648157353
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-0.5166047365590571 0.7641033353626657 -0.2862677570028208 -0.68254820978656
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KLF4_f2
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0.30861857265872605 -2.254321000121579 0.13505703522674192 0.3285194224375633
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-
-1.227018967707036 -4.814127713368663 1.3059890687390967 -4.908681463544344
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-2.443469374521196 -4.648238485031404 1.3588686548279805 -4.441801801188402
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-2.7177827948276123 -3.8073538975356565 1.356272809724262 -3.504104725510225
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-0.5563232977367343 0.5340697765121405 -3.61417723090579 0.5270259776377405
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-1.8687622060887386 -4.381483976582316 1.337932245336098 -3.815629658877517
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-2.045671123823928 -2.384975142213679 0.7198551207724355 0.5449254135616948
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-1.373157530374372 -3.0063112097748217 1.285188335493552 -2.5026044231773543
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-2.1030513122772208 -1.8941348100402244 1.249265758393991 -1.4284210948906104
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-1.3277128628152939 0.8982415633049462 -0.8080773665408135 -0.18161647647456935
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-
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GABPA_f1
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> GABPA_f1
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-0.1106670158341858 0.013801606113892391 0.6054596108973699 -1.3518085041421573
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0.37030668921643345 0.15761121480429963 0.009069314183831202 -0.9888619717703562
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0.47526546359546684 -0.3011678534572083 0.4031522994412777 -1.8638752827041059
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@@ -36,3 +12,27 @@ GABPA_f1
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-1.3716559438167257 -0.2761401935045069 -1.8504445165866068 1.0404320473626856
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-0.5440863133031895 -0.48103682561971345 0.907381908447086 -1.1280642594012078
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0.10557340209290218 -0.01814819455289191 0.4381106695354074 -1.0304105539540915
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KLF4_f2
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0.30861857265872605 -2.254321000121579 0.13505703522674192 0.3285194224375633
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-1.227018967707036 -4.814127713368663 1.3059890687390967 -4.908681463544344
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-2.443469374521196 -4.648238485031404 1.3588686548279805 -4.441801801188402
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-2.7177827948276123 -3.8073538975356565 1.356272809724262 -3.504104725510225
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-0.5563232977367343 0.5340697765121405 -3.61417723090579 0.5270259776377405
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-1.8687622060887386 -4.381483976582316 1.337932245336098 -3.815629658877517
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-2.045671123823928 -2.384975142213679 0.7198551207724355 0.5449254135616948
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-1.373157530374372 -3.0063112097748217 1.285188335493552 -2.5026044231773543
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-2.1030513122772208 -1.8941348100402244 1.249265758393991 -1.4284210948906104
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-1.3277128628152939 0.8982415633049462 -0.8080773665408135 -0.18161647647456935
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SP1_f1
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-0.24435707885585292 -0.674823404693731 0.8657012535789866 -1.1060188862599287
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-1.0631255752097797 -2.111925969423868 1.0960627561110403 -0.6138563775211977
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-0.3872276234760535 -2.9739851913218045 1.1807800242010378 -4.338927525031566
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-4.563896055436894 -2.9161633002532277 1.3684371349982638 -5.077972423609655
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-2.2369752892820083 -3.7196436313301846 1.3510439136452734 -4.889930670508233
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-0.07473964149330865 0.944919654762011 -2.6246857648086044 -0.8510983487822436
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-1.9643526491643322 -2.978402770880115 1.3113096718240573 -2.324334259499025
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-4.0155484139655835 -3.1384268078096667 1.3387488589788057 -2.084673903537648
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-0.44509385828355363 -2.2510053061629702 1.1265431574368685 -1.7780413702431372
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-1.1896356092245048 -1.2251832285630027 1.1636760063747527 -1.6080243648157353
|
38
|
+
-0.5166047365590571 0.7641033353626657 -0.2862677570028208 -0.68254820978656
|
@@ -1,28 +1,4 @@
|
|
1
|
-
>
|
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.
|
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.
|
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.
|
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.
|
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.
|
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.
|
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.
|
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.
|
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-
|
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.
|
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.
|
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
|