--- !ruby/object:Gem::Specification
name: macroape
version: !ruby/object:Gem::Version
  version: 3.3.6
  prerelease: 
platform: ruby
authors:
- Ilya Vorontsov
autorequire: 
bindir: bin
cert_chain: []
date: 2012-09-11 00:00:00.000000000 Z
dependencies:
- !ruby/object:Gem::Dependency
  name: bioinform
  requirement: !ruby/object:Gem::Requirement
    none: false
    requirements:
    - - ! '>='
      - !ruby/object:Gem::Version
        version: 0.1.7
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    none: false
    requirements:
    - - ! '>='
      - !ruby/object:Gem::Version
        version: 0.1.7
description: Macroape is an abbreviation for MAtrix CompaRisOn by Approximate P-value
  Estimation. It's a bioinformatic tool for evaluating similarity measure and best
  alignment between a pair of Position Weight Matrices(PWM), finding thresholds by
  P-values and inside out and even searching a collection of motifs for the most similar
  ones. Used approach and application described in manual at https://docs.google.com/document/pub?id=1_jsxhMNzMzy4d2d_byAd3n6Szg5gEcqG_Sf7w9tEqWw
email:
- prijutme4ty@gmail.com
executables:
- align_motifs
- eval_alignment
- eval_similarity
- find_pvalue
- find_threshold
- preprocess_collection
- scan_collection
extensions: []
extra_rdoc_files: []
files:
- .gitignore
- Gemfile
- LICENSE
- README.md
- Rakefile.rb
- TODO.txt
- benchmark/similarity_benchmark.rb
- bin/align_motifs
- bin/eval_alignment
- bin/eval_similarity
- bin/find_pvalue
- bin/find_threshold
- bin/preprocess_collection
- bin/scan_collection
- lib/macroape.rb
- lib/macroape/aligned_pair_intersection.rb
- lib/macroape/cli.rb
- lib/macroape/cli/align_motifs.rb
- lib/macroape/cli/eval_alignment.rb
- lib/macroape/cli/eval_similarity.rb
- lib/macroape/cli/find_pvalue.rb
- lib/macroape/cli/find_threshold.rb
- lib/macroape/cli/preprocess_collection.rb
- lib/macroape/cli/scan_collection.rb
- lib/macroape/counting.rb
- lib/macroape/pwm_compare.rb
- lib/macroape/pwm_compare_aligned.rb
- lib/macroape/version.rb
- macroape.gemspec
- spec/count_distribution_spec.rb
- spec/spec_helper.rb
- test/align_motifs_test.rb
- test/data/AHR_si.pat
- test/data/KLF3_f1.pat
- test/data/KLF3_f1.pcm
- test/data/KLF4_f2.pat
- test/data/KLF4_f2.pcm
- test/data/KLF4_f2_scan_results_all.txt
- test/data/KLF4_f2_scan_results_default_cutoff.txt
- test/data/KLF4_f2_scan_results_precise_mode.txt
- test/data/SP1_f1.pat
- test/data/SP1_f1.pcm
- test/data/SP1_f1_revcomp.pat
- test/data/SP1_f1_revcomp.pcm
- test/data/test_collection.yaml
- test/data/test_collection/GABPA_f1.pat
- test/data/test_collection/KLF4_f2.pat
- test/data/test_collection/SP1_f1.pat
- test/data/test_collection_pcm/GABPA_f1.pcm
- test/data/test_collection_pcm/KLF4_f2.pcm
- test/data/test_collection_pcm/SP1_f1.pcm
- test/data/test_collection_single_file.txt
- test/data/test_collection_single_file_pcm.txt
- test/eval_alignment_test.rb
- test/eval_similarity_test.rb
- test/find_pvalue_test.rb
- test/find_threshold_test.rb
- test/preprocess_collection_test.rb
- test/scan_collection_test.rb
- test/test_helper.rb
homepage: http://autosome.ru/macroape/
licenses: []
post_install_message: 
rdoc_options: []
require_paths:
- lib
required_ruby_version: !ruby/object:Gem::Requirement
  none: false
  requirements:
  - - ! '>='
    - !ruby/object:Gem::Version
      version: '0'
required_rubygems_version: !ruby/object:Gem::Requirement
  none: false
  requirements:
  - - ! '>='
    - !ruby/object:Gem::Version
      version: '0'
requirements: []
rubyforge_project: 
rubygems_version: 1.8.24
signing_key: 
specification_version: 3
summary: PWM comparison tool using MACROAPE approach
test_files:
- spec/count_distribution_spec.rb
- spec/spec_helper.rb
- test/align_motifs_test.rb
- test/data/AHR_si.pat
- test/data/KLF3_f1.pat
- test/data/KLF3_f1.pcm
- test/data/KLF4_f2.pat
- test/data/KLF4_f2.pcm
- test/data/KLF4_f2_scan_results_all.txt
- test/data/KLF4_f2_scan_results_default_cutoff.txt
- test/data/KLF4_f2_scan_results_precise_mode.txt
- test/data/SP1_f1.pat
- test/data/SP1_f1.pcm
- test/data/SP1_f1_revcomp.pat
- test/data/SP1_f1_revcomp.pcm
- test/data/test_collection.yaml
- test/data/test_collection/GABPA_f1.pat
- test/data/test_collection/KLF4_f2.pat
- test/data/test_collection/SP1_f1.pat
- test/data/test_collection_pcm/GABPA_f1.pcm
- test/data/test_collection_pcm/KLF4_f2.pcm
- test/data/test_collection_pcm/SP1_f1.pcm
- test/data/test_collection_single_file.txt
- test/data/test_collection_single_file_pcm.txt
- test/eval_alignment_test.rb
- test/eval_similarity_test.rb
- test/find_pvalue_test.rb
- test/find_threshold_test.rb
- test/preprocess_collection_test.rb
- test/scan_collection_test.rb
- test/test_helper.rb