WingenderTFClass 0.1.0
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- checksums.yaml +7 -0
- data/.gitignore +9 -0
- data/.travis.yml +4 -0
- data/Gemfile +4 -0
- data/README.md +36 -0
- data/Rakefile +10 -0
- data/WingenderTFClass.gemspec +32 -0
- data/bin/console +14 -0
- data/bin/setup +7 -0
- data/lib/WingenderTFClass.rb +6 -0
- data/lib/WingenderTFClass/motif_family_recognizer.rb +96 -0
- data/lib/WingenderTFClass/obo/term.rb +110 -0
- data/lib/WingenderTFClass/obo/tf_classification.rb +69 -0
- data/lib/WingenderTFClass/rake/WingenderClassification.rake +64 -0
- data/lib/WingenderTFClass/source_data/TFClass_ontologies_temp.zip +0 -0
- data/lib/WingenderTFClass/source_data/TFOntologies/TFClass_human.obo +41262 -0
- data/lib/WingenderTFClass/source_data/TFOntologies/TFClass_mouse.obo +23595 -0
- data/lib/WingenderTFClass/source_data/uniprot_infos/human.tsv +149031 -0
- data/lib/WingenderTFClass/source_data/uniprot_infos/mouse.tsv +79005 -0
- data/lib/WingenderTFClass/source_data_old/TFClass_ontologies_temp.zip +0 -0
- data/lib/WingenderTFClass/source_data_old/TFOntologies/TFClass_human.obo +41262 -0
- data/lib/WingenderTFClass/source_data_old/TFOntologies/TFClass_mouse.obo +23595 -0
- data/lib/WingenderTFClass/source_data_old/uniprot_ID_to_AC.tsv +226840 -0
- data/lib/WingenderTFClass/uniprot_info.rb +22 -0
- data/lib/WingenderTFClass/version.rb +3 -0
- metadata +111 -0
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module WingenderTFClass
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UniprotInfo = Struct.new(:uniprot_ac, :uniprot_id) do
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def self.from_string(line)
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uniprot_ac, uniprot_id = line.chomp.split("\t", 2)
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self.new(uniprot_ac, uniprot_id)
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end
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def self.each_in_file(filename, &block)
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File.readlines(filename).drop(1).map{|line| self.from_string(line) }.each(&block)
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end
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def self.uniprot_ac_list_by_id_from_file(filename)
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result = self.each_in_file(filename)
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.group_by(&:uniprot_id)
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.map{|uniprot_id, uniprots|
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[uniprot_id, uniprots.map(&:uniprot_ac)]
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}.to_h
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result.default_proc = ->(h,k){h[k] = [] }
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result
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end
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end
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end
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metadata
ADDED
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--- !ruby/object:Gem::Specification
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name: WingenderTFClass
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version: !ruby/object:Gem::Version
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version: 0.1.0
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platform: ruby
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authors:
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- prijutme4ty
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autorequire:
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bindir: exe
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cert_chain: []
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date: 2015-10-18 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bundler
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requirement: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '1.10'
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type: :development
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '1.10'
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- !ruby/object:Gem::Dependency
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name: rake
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requirement: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '10.0'
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type: :development
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '10.0'
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- !ruby/object:Gem::Dependency
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name: minitest
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requirement: !ruby/object:Gem::Requirement
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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version: '0'
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type: :development
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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version: '0'
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description: This gem allows to retrieve information for a transcription factor from
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Wingender's TFClass ontology.
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email:
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- prijutme4ty@gmail.com
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executables: []
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extensions: []
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extra_rdoc_files: []
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files:
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- ".gitignore"
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- ".travis.yml"
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- Gemfile
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- README.md
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- Rakefile
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- WingenderTFClass.gemspec
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- bin/console
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- bin/setup
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- lib/WingenderTFClass.rb
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- lib/WingenderTFClass/motif_family_recognizer.rb
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- lib/WingenderTFClass/obo/term.rb
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- lib/WingenderTFClass/obo/tf_classification.rb
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- lib/WingenderTFClass/rake/WingenderClassification.rake
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- lib/WingenderTFClass/source_data/TFClass_ontologies_temp.zip
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- lib/WingenderTFClass/source_data/TFOntologies/TFClass_human.obo
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- lib/WingenderTFClass/source_data/TFOntologies/TFClass_mouse.obo
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- lib/WingenderTFClass/source_data/uniprot_infos/human.tsv
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- lib/WingenderTFClass/source_data/uniprot_infos/mouse.tsv
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- lib/WingenderTFClass/source_data_old/TFClass_ontologies_temp.zip
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- lib/WingenderTFClass/source_data_old/TFOntologies/TFClass_human.obo
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- lib/WingenderTFClass/source_data_old/TFOntologies/TFClass_mouse.obo
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- lib/WingenderTFClass/source_data_old/uniprot_ID_to_AC.tsv
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- lib/WingenderTFClass/uniprot_info.rb
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- lib/WingenderTFClass/version.rb
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homepage: https://github.com/VorontsovIE/WingenderTFClass
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licenses: []
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metadata: {}
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post_install_message:
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rdoc_options: []
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require_paths:
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- lib
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required_ruby_version: !ruby/object:Gem::Requirement
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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version: '0'
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required_rubygems_version: !ruby/object:Gem::Requirement
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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version: '0'
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requirements: []
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rubyforge_project:
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rubygems_version: 2.4.6
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signing_key:
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specification_version: 4
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summary: Gem to acquire TFClass protein class/family/subfamily/etc for a transcription
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factor by its UniprotID.
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test_files: []
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