mizlab 0.1.5 → 0.1.6

checksums.yaml

@@ -1,7 +1,7 @@
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data/Gemfile

@@ -5,10 +5,7 @@ source "https://rubygems.org"
 # Specify your gem's dependencies in mizlab.gemspec
 gemspec
 
-gem "rake", "~> 13.0"
-
-gem "minitest", "~> 5.0"
-
-gem "yard", "~> 0.9"
-
-gem "bio"
+# gem "rake", "~> 13.0"
+# gem "minitest", "~> 5.0"
+# gem "yard", "~> 0.9"
+# gem "bio", "~> 2.0.0"

data/README.md

@@ -1,10 +1,10 @@
 [![Test](https://github.com/MizLab/Mizlab-ruby/actions/workflows/minitest.yml/badge.svg)](https://github.com/MizLab/Mizlab-ruby/actions/workflows/minitest.yml)
 [![Build page](https://github.com/MizLab/Mizlab-ruby/actions/workflows/yardoc.yml/badge.svg)](https://github.com/MizLab/Mizlab-ruby/actions/workflows/yardoc.yml)
+[![Gem Version](https://badge.fury.io/rb/mizlab.svg)](https://badge.fury.io/rb/mizlab)
 
 # Mizlab-ruby
 
-This gem is for easy handling of the processes used in our labolatory.
-
+This gem is for easy handling of the processes used in our laboratory.
 
 ## Installation
 
@@ -14,7 +14,7 @@ Install it yourself as:
 gem install mizlab
 ```
 
-or add below to your application's Gemfile:
+Or add below to your application's Gemfile:
 
 ```ruby
 gem 'mizlab'
@@ -38,7 +38,7 @@ To install this gem onto your local machine, run `bundle exec rake install`. To
 
 ## Contributing
 
-Bug reports and pull requests are welcome on GitHub at https://github.com/[USERNAME]/mizlab.
+Bug reports and pull requests are welcome on GitHub at https://github.com/MizLab/Mizlab-ruby
 
 ## License
 

data/lib/mizlab/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Mizlab
-  VERSION = "0.1.5"
+  VERSION = "0.1.6"
 end

data/lib/mizlab.rb

@@ -4,6 +4,7 @@ require_relative "mizlab/version"
 require "set"
 require "bio"
 require "stringio"
+require "rexml/document"
 
 module Mizlab
   class << self
@@ -138,6 +139,23 @@ module Mizlab
       return local_pattern_list
     end
 
+    # Fetch Taxonomy information from Taxonomy ID. can be give block too.
+    # @param  [String/Integer] taxonid Taxonomy ID, or Array of its.
+    # @return [Hash] Taxonomy informations.
+    # @yield  [Hash] Taxonomy informations.
+    def fetch_taxon(taxonid)
+      taxonid = taxonid.is_a?(Array) ? taxonid : [taxonid]
+      taxonid.each do |id|
+        obj = Bio::NCBI::REST::EFetch.taxonomy(id, "xml")
+        hashed = xml_to_hash(REXML::Document.new(obj).root)
+        if block_given?
+          yield hashed[:TaxaSet][:Taxon][:LineageEx][:Taxon]
+        else
+          return hashed[:TaxaSet][:Taxon][:LineageEx][:Taxon]
+        end
+      end
+    end
+
     private
 
     def fetch_protein(accession)
@@ -243,5 +261,21 @@ module Mizlab
         yield e
       end
     end
+
+    # Convert XML to Hash.
+    # @param  [REXML::Document] element XML object.
+    # @return [Hash] Hash that converted from xml.
+    def xml_to_hash(element)
+      value = (if element.has_elements?
+        children = {}
+        element.each_element do |e|
+          children.merge!(xml_to_hash(e)) { |k, v1, v2| v1.is_a?(Array) ? v1 << v2 : [v1, v2] }
+        end
+        children
+      else
+        element.text
+      end)
+      return { element.name.to_sym => value }
+    end
   end
 end

data/mizlab.gemspec

@@ -29,8 +29,14 @@ Gem::Specification.new do |spec|
   spec.executables   = spec.files.grep(%r{\Aexe/}) { |f| File.basename(f) }
   spec.require_paths = ["lib"]
 
-  # Uncomment to register a new dependency of your gem
-  # spec.add_dependency "example-gem", "~> 1.0"
+  # Dependency
+  spec.add_dependency "bio", "~> 2.0.0"
+  spec.add_dependency "rexml", ">= 0"
+
+  # Dependency (for development)
+  spec.add_development_dependency "rake", "~> 13.0"
+  spec.add_development_dependency "yard", "~> 0.9"
+  spec.add_development_dependency "minitest", "~> 5.0"
 
   # For more information and examples about making a new gem, checkout our
   # guide at: https://bundler.io/guides/creating_gem.html

metadata

@@ -1,15 +1,85 @@
 --- !ruby/object:Gem::Specification
 name: mizlab
 version: !ruby/object:Gem::Version
-  version: 0.1.5
+  version: 0.1.6
 platform: ruby
 authors:
 - Omochice
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2021-10-26 00:00:00.000000000 Z
-dependencies: []
+date: 2021-10-28 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.0.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.0.0
+- !ruby/object:Gem::Dependency
+  name: rexml
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '13.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '13.0'
+- !ruby/object:Gem::Dependency
+  name: yard
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.9'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.9'
+- !ruby/object:Gem::Dependency
+  name: minitest
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '5.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '5.0'
 description: The tools for our laboratory
 email:
 - mochice.mls.ntl@gmail.com