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.
- data/README.md +2 -2
- data/Rakefile.rb +6 -6
- data/TODO.txt +23 -3
- data/benchmark/similarity_benchmark.rb +18 -18
- data/lib/macroape/aligned_pair_intersection.rb +4 -4
- data/lib/macroape/cli/align_motifs.rb +34 -28
- data/lib/macroape/cli/eval_alignment.rb +73 -47
- data/lib/macroape/cli/eval_similarity.rb +65 -40
- data/lib/macroape/cli/find_pvalue.rb +30 -34
- data/lib/macroape/cli/find_threshold.rb +52 -41
- data/lib/macroape/cli/preprocess_collection.rb +68 -58
- data/lib/macroape/cli/scan_collection.rb +89 -73
- data/lib/macroape/cli.rb +184 -1
- data/lib/macroape/counting.rb +31 -5
- data/lib/macroape/pwm_compare.rb +8 -2
- data/lib/macroape/pwm_compare_aligned.rb +15 -10
- data/lib/macroape/version.rb +2 -1
- data/macroape.gemspec +2 -1
- data/spec/count_distribution_spec.rb +11 -11
- data/test/align_motifs_test.rb +16 -4
- data/test/data/{AHR_si.pat → AHR_si.pwm} +0 -0
- data/test/data/{KLF3_f1.pat → KLF3_f1.pwm} +0 -0
- data/test/data/{KLF4_f2.pat → KLF4_f2.pwm} +0 -0
- data/test/data/KLF4_f2_scan_results_all.txt +1 -2
- data/test/data/KLF4_f2_scan_results_default_cutoff.txt +1 -2
- data/test/data/KLF4_f2_scan_results_precise_mode.txt +1 -2
- data/test/data/KLF4_f2_scan_results_weak_threshold.txt +2 -0
- data/test/data/{SP1_f1.pat → SP1_f1.pwm} +0 -0
- data/test/data/{SP1_f1_revcomp.pat → SP1_f1_revcomp.pwm} +0 -0
- data/test/data/collection_pcm_without_thresholds.yaml +186 -183
- data/test/data/collection_without_thresholds.yaml +186 -183
- data/test/data/{medium_motif.pat → medium_motif.pwm} +0 -0
- data/test/data/{short_motif.pat → short_motif.pwm} +0 -0
- data/test/data/test_collection/{GABPA_f1.pat → GABPA_f1.pwm} +0 -0
- data/test/data/test_collection/{KLF4_f2.pat → KLF4_f2.pwm} +0 -0
- data/test/data/test_collection/{SP1_f1.pat → SP1_f1.pwm} +0 -0
- data/test/data/test_collection.yaml +179 -176
- data/test/data/test_collection_weak.yaml +214 -0
- data/test/eval_alignment_test.rb +97 -21
- data/test/eval_similarity_test.rb +104 -26
- data/test/find_pvalue_test.rb +22 -9
- data/test/find_threshold_test.rb +76 -25
- data/test/preprocess_collection_test.rb +16 -21
- data/test/scan_collection_test.rb +26 -14
- data/test/test_helper.rb +96 -12
- metadata +44 -24
data/test/test_helper.rb
CHANGED
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@@ -12,7 +12,7 @@ require_relative '../lib/macroape/cli/eval_alignment'
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require_relative '../lib/macroape/cli/preprocess_collection'
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require_relative '../lib/macroape/cli/scan_collection'
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require_relative '../lib/macroape/cli/align_motifs'
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-
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+
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module Helpers
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# from minitest
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def self.capture_io(&block)
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@@ -25,25 +25,40 @@ module Helpers
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$stdout = orig_stdout
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$stderr = orig_stderr
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end
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-
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+
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def self.suppress_output(&block)
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orig_stdout, orig_stderr = $stdout, $stderr
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captured_stdout, captured_stderr = StringIO.new, StringIO.new
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$stdout, $stderr = captured_stdout, captured_stderr
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yield
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ensure
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$stdout = orig_stdout
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$stderr = orig_stderr
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end
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# Method stubs $stdin not STDIN !
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def self.provide_stdin(input, &block)
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orig_stdin = $stdin
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$stdin = StringIO.new(input)
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yield
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ensure
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ensure
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$stdin = orig_stdin
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end
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-
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+
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def self.capture_output(&block)
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capture_io(&block)[:stdout]
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end
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def self.capture_stderr(&block)
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capture_io(&block)[:stderr]
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end
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-
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+
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# aaa\tbbb\nccc\tddd ==> [['aaa','bbb'],['ccc','ddd']]
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def self.split_on_lines(str)
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str.lines.map{|line| line.strip.split("\t")}
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end
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def self.obtain_pvalue_by_threshold(args)
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find_pvalue_output(args).
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find_pvalue_output(args).last.last
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end
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def self.exec_cmd(executable, param_list)
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"ruby -I #{$lib_folder} #{$lib_folder}/../bin/#{executable} #{param_list}"
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@@ -52,25 +67,94 @@ module Helpers
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capture_output{ Macroape::CLI::FindThreshold.main(param_list.shellsplit) }
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end
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def self.align_motifs_output(param_list)
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capture_output{ Macroape::CLI::AlignMotifs.main(param_list.shellsplit)
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split_on_lines( capture_output{ Macroape::CLI::AlignMotifs.main(param_list.shellsplit)} )
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end
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def self.find_pvalue_output(param_list)
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capture_output{ Macroape::CLI::FindPValue.main(param_list.shellsplit) }
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capture_output{ Macroape::CLI::FindPValue.main(param_list.shellsplit)} .lines.to_a.map(&:strip).reject{|line| line.start_with? '#' }.reject(&:empty?).map{|line|line.split("\t")}
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end
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def self.eval_similarity_output(param_list)
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capture_output{ Macroape::CLI::EvalSimilarity.main(param_list.shellsplit)
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capture_output{ Macroape::CLI::EvalSimilarity.main(param_list.shellsplit)}
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end
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def self.eval_alignment_output(param_list)
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capture_output{ Macroape::CLI::EvalAlignment.main(param_list.shellsplit)
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capture_output{ Macroape::CLI::EvalAlignment.main(param_list.shellsplit)}
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end
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def self.scan_collection_output(param_list)
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capture_output{ Macroape::CLI::ScanCollection.main(param_list.shellsplit) }
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capture_output{ Macroape::CLI::ScanCollection.main(param_list.shellsplit) }.lines.to_a.map(&:strip).reject{|line| line.start_with? '#' }.reject(&:empty?).join("\n")
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end
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def self.scan_collection_stderr(param_list)
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capture_stderr{ Macroape::CLI::ScanCollection.main(param_list.shellsplit) }
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end
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def self.run_preprocess_collection(param_list)
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Macroape::CLI::PreprocessCollection.main(param_list.shellsplit)
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suppress_output{ Macroape::CLI::PreprocessCollection.main(param_list.shellsplit) }
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end
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def parse_similarity_infos_string(info_string)
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infos = {}
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info_string.lines.map(&:strip).reject{|line| line.start_with?('#')}.reject(&:empty?).each do |line|
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key, value = line.split
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case key
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when 'S' then infos[:similarity] = value
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when 'D' then infos[:distance] = value
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when 'L' then infos[:length] = value
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when 'SH' then infos[:shift] = value
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when 'OR' then infos[:orientation] = value
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when 'W' then infos[:words_recognized_by_both] = value
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when 'W1' then infos[:words_recognized_by_first] = value
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when 'P1' then infos[:pvalue_recognized_by_first] = value
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when 'T1' then infos[:threshold_first] = value
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when 'W2' then infos[:words_recognized_by_second] = value
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when 'P2' then infos[:pvalue_recognized_by_second] = value
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when 'T2' then infos[:threshold_second] = value
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when 'A1' then infos[:matrix_first_alignment] = value
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when 'A2' then infos[:matrix_second_alignment] = value
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when 'V' then infos[:discretization] = value
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end
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end
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infos
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end
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def assert_similarity_info_output(expected_info, info_string)
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infos = parse_similarity_infos_string(info_string)
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expected_info.each do |key, value|
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assert_equal value.to_s, infos[key]
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end
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end
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def parse_threshold_infos_string(infos_string)
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infos = []
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infos_string.lines.map(&:strip).reject{|line| line.start_with?('#')}.reject(&:empty?).each do |line|
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info_data = line.split
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if info_data.size == 4
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requested_pvalue, real_pvalue, number_of_recognized_words, threshold = info_data
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info = {requested_pvalue: requested_pvalue,
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real_pvalue: real_pvalue,
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number_of_recognized_words: number_of_recognized_words,
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threshold: threshold }
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elsif info_data.size == 3
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requested_pvalue, real_pvalue, threshold = info_data
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info = {requested_pvalue: requested_pvalue,
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real_pvalue: real_pvalue,
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threshold: threshold }
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else
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raise 'can\'t parse threshold infos table'
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end
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infos << info
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end
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infos
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end
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def assert_threshold_info_output(*expected_infos, info_string)
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infos = parse_threshold_infos_string(info_string)
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expected_infos.zip(infos).each do |expected_info, info|
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assert_not_nil info
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expected_info.each do |key, value|
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assert_equal value.to_s, info[key]
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end
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end
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end
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end
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metadata
CHANGED
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@@ -1,7 +1,7 @@
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1
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--- !ruby/object:Gem::Specification
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name: macroape
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version: !ruby/object:Gem::Version
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-
version: 3.3.
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version: 3.3.8
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prerelease:
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platform: ruby
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authors:
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@@ -9,7 +9,7 @@ authors:
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2012-
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date: 2012-12-07 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bioinform
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@@ -18,7 +18,7 @@ dependencies:
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requirements:
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- - '='
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- !ruby/object:Gem::Version
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version: 0.1.
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version: 0.1.9
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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@@ -26,7 +26,23 @@ dependencies:
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requirements:
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- - '='
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- !ruby/object:Gem::Version
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version: 0.1.
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version: 0.1.9
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- !ruby/object:Gem::Dependency
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name: docopt
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requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - '='
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- !ruby/object:Gem::Version
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version: 0.5.0
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - '='
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- !ruby/object:Gem::Version
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version: 0.5.0
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description: Macroape is an abbreviation for MAtrix CompaRisOn by Approximate P-value
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Estimation. It's a bioinformatic tool for evaluating similarity measure and best
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alignment between a pair of Position Weight Matrices(PWM), finding thresholds by
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@@ -78,31 +94,33 @@ files:
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- spec/count_distribution_spec.rb
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- spec/spec_helper.rb
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96
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- test/align_motifs_test.rb
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-
- test/data/AHR_si.
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-
- test/data/KLF3_f1.pat
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97
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- test/data/AHR_si.pwm
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98
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- test/data/KLF3_f1.pcm
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-
- test/data/
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- test/data/KLF3_f1.pwm
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- test/data/KLF4_f2.pcm
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- test/data/KLF4_f2.pwm
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- test/data/KLF4_f2_scan_results_all.txt
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- test/data/KLF4_f2_scan_results_default_cutoff.txt
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- test/data/KLF4_f2_scan_results_precise_mode.txt
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-
- test/data/
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- test/data/KLF4_f2_scan_results_weak_threshold.txt
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- test/data/SP1_f1.pcm
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-
- test/data/
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- test/data/SP1_f1.pwm
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108
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- test/data/SP1_f1_revcomp.pcm
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- test/data/SP1_f1_revcomp.pwm
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- test/data/collection_pcm_without_thresholds.yaml
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- test/data/collection_without_thresholds.yaml
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-
- test/data/medium_motif.
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-
- test/data/short_motif.
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112
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+
- test/data/medium_motif.pwm
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113
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- test/data/short_motif.pwm
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- test/data/test_collection.yaml
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98
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-
- test/data/test_collection/GABPA_f1.
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99
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-
- test/data/test_collection/KLF4_f2.
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-
- test/data/test_collection/SP1_f1.
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- test/data/test_collection/GABPA_f1.pwm
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- test/data/test_collection/KLF4_f2.pwm
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- test/data/test_collection/SP1_f1.pwm
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- test/data/test_collection_pcm/GABPA_f1.pcm
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119
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- test/data/test_collection_pcm/KLF4_f2.pcm
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- test/data/test_collection_pcm/SP1_f1.pcm
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- test/data/test_collection_single_file.txt
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- test/data/test_collection_single_file_pcm.txt
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+
- test/data/test_collection_weak.yaml
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106
124
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- test/eval_alignment_test.rb
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107
125
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- test/eval_similarity_test.rb
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108
126
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- test/find_pvalue_test.rb
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@@ -138,31 +156,33 @@ test_files:
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138
156
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- spec/count_distribution_spec.rb
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139
157
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- spec/spec_helper.rb
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140
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- test/align_motifs_test.rb
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141
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-
- test/data/AHR_si.
|
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142
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-
- test/data/KLF3_f1.pat
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159
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+
- test/data/AHR_si.pwm
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143
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- test/data/KLF3_f1.pcm
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144
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-
- test/data/
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- test/data/KLF3_f1.pwm
|
|
145
162
|
- test/data/KLF4_f2.pcm
|
|
163
|
+
- test/data/KLF4_f2.pwm
|
|
146
164
|
- test/data/KLF4_f2_scan_results_all.txt
|
|
147
165
|
- test/data/KLF4_f2_scan_results_default_cutoff.txt
|
|
148
166
|
- test/data/KLF4_f2_scan_results_precise_mode.txt
|
|
149
|
-
- test/data/
|
|
167
|
+
- test/data/KLF4_f2_scan_results_weak_threshold.txt
|
|
150
168
|
- test/data/SP1_f1.pcm
|
|
151
|
-
- test/data/
|
|
169
|
+
- test/data/SP1_f1.pwm
|
|
152
170
|
- test/data/SP1_f1_revcomp.pcm
|
|
171
|
+
- test/data/SP1_f1_revcomp.pwm
|
|
153
172
|
- test/data/collection_pcm_without_thresholds.yaml
|
|
154
173
|
- test/data/collection_without_thresholds.yaml
|
|
155
|
-
- test/data/medium_motif.
|
|
156
|
-
- test/data/short_motif.
|
|
174
|
+
- test/data/medium_motif.pwm
|
|
175
|
+
- test/data/short_motif.pwm
|
|
157
176
|
- test/data/test_collection.yaml
|
|
158
|
-
- test/data/test_collection/GABPA_f1.
|
|
159
|
-
- test/data/test_collection/KLF4_f2.
|
|
160
|
-
- test/data/test_collection/SP1_f1.
|
|
177
|
+
- test/data/test_collection/GABPA_f1.pwm
|
|
178
|
+
- test/data/test_collection/KLF4_f2.pwm
|
|
179
|
+
- test/data/test_collection/SP1_f1.pwm
|
|
161
180
|
- test/data/test_collection_pcm/GABPA_f1.pcm
|
|
162
181
|
- test/data/test_collection_pcm/KLF4_f2.pcm
|
|
163
182
|
- test/data/test_collection_pcm/SP1_f1.pcm
|
|
164
183
|
- test/data/test_collection_single_file.txt
|
|
165
184
|
- test/data/test_collection_single_file_pcm.txt
|
|
185
|
+
- test/data/test_collection_weak.yaml
|
|
166
186
|
- test/eval_alignment_test.rb
|
|
167
187
|
- test/eval_similarity_test.rb
|
|
168
188
|
- test/find_pvalue_test.rb
|