RubyGems - WingenderTFClass - Versions diffs - 0.1.0 - Mend

WingenderTFClass 0.1.0

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Files changed (26) hide show

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

data/lib/WingenderTFClass/uniprot_info.rb ADDED Viewed

@@ -0,0 +1,22 @@
+module WingenderTFClass
+  UniprotInfo = Struct.new(:uniprot_ac, :uniprot_id) do
+    def self.from_string(line)
+      uniprot_ac, uniprot_id = line.chomp.split("\t", 2)
+      self.new(uniprot_ac, uniprot_id)
+    end
+    def self.each_in_file(filename, &block)
+      File.readlines(filename).drop(1).map{|line| self.from_string(line) }.each(&block)
+    end
+    def self.uniprot_ac_list_by_id_from_file(filename)
+      result = self.each_in_file(filename)
+                  .group_by(&:uniprot_id)
+                  .map{|uniprot_id, uniprots|
+                    [uniprot_id, uniprots.map(&:uniprot_ac)]
+                  }.to_h
+      result.default_proc = ->(h,k){h[k] = [] }
+      result
+    end
+  end
+end

data/lib/WingenderTFClass/version.rb ADDED Viewed

@@ -0,0 +1,3 @@
+module WingenderTFClass
+  VERSION = "0.1.0"
+end

metadata ADDED Viewed

@@ -0,0 +1,111 @@
+--- !ruby/object:Gem::Specification
+name: WingenderTFClass
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- prijutme4ty
+autorequire:
+bindir: exe
+cert_chain: []
+date: 2015-10-18 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.10'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.10'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+- !ruby/object:Gem::Dependency
+  name: minitest
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+description: This gem allows to retrieve information for a transcription factor from
+  Wingender's TFClass ontology.
+email:
+- prijutme4ty@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".travis.yml"
+- Gemfile
+- README.md
+- Rakefile
+- WingenderTFClass.gemspec
+- bin/console
+- bin/setup
+- lib/WingenderTFClass.rb
+- lib/WingenderTFClass/motif_family_recognizer.rb
+- lib/WingenderTFClass/obo/term.rb
+- lib/WingenderTFClass/obo/tf_classification.rb
+- lib/WingenderTFClass/rake/WingenderClassification.rake
+- lib/WingenderTFClass/source_data/TFClass_ontologies_temp.zip
+- lib/WingenderTFClass/source_data/TFOntologies/TFClass_human.obo
+- lib/WingenderTFClass/source_data/TFOntologies/TFClass_mouse.obo
+- lib/WingenderTFClass/source_data/uniprot_infos/human.tsv
+- lib/WingenderTFClass/source_data/uniprot_infos/mouse.tsv
+- lib/WingenderTFClass/source_data_old/TFClass_ontologies_temp.zip
+- lib/WingenderTFClass/source_data_old/TFOntologies/TFClass_human.obo
+- lib/WingenderTFClass/source_data_old/TFOntologies/TFClass_mouse.obo
+- lib/WingenderTFClass/source_data_old/uniprot_ID_to_AC.tsv
+- lib/WingenderTFClass/uniprot_info.rb
+- lib/WingenderTFClass/version.rb
+homepage: https://github.com/VorontsovIE/WingenderTFClass
+licenses: []
+metadata: {}
+post_install_message:
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project:
+rubygems_version: 2.4.6
+signing_key:
+specification_version: 4
+summary: Gem to acquire TFClass protein class/family/subfamily/etc for a transcription
+  factor by its UniprotID.
+test_files: []