mizlab 0.1.5 → 0.1.6
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- checksums.yaml +4 -4
- data/Gemfile +4 -7
- data/README.md +4 -4
- data/lib/mizlab/version.rb +1 -1
- data/lib/mizlab.rb +34 -0
- data/mizlab.gemspec +8 -2
- metadata +73 -3
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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---
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SHA256:
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metadata.gz:
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data.tar.gz:
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metadata.gz: '0997e1a56ba6b17aa4eedc2fd89e84462e3ac2d3f51c1c251221a0fc7613ff66'
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data.tar.gz: aaac55320663e3b8fef03c5518d73156ea3a1880736936c8debb1a6eb9d60935
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: a5e073bceea54fd25ad99e80c35052732c265a6e827b8e23bcf4f2bc21f3b03095243d5e9b718bf6b521ae8097f5059b72a15cc32ec67e7bfe534e3b8c7d35bc
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7
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data.tar.gz: 61f1545fd3218ce1a74b030a6a64718964a8129f30587deaebeb038cadfe82991b9d7356751129ba92df751278193d5a1cf92c147790e8a88008bb285fa665c8
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data/Gemfile
CHANGED
@@ -5,10 +5,7 @@ source "https://rubygems.org"
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5
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# Specify your gem's dependencies in mizlab.gemspec
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gemspec
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gem "rake", "~> 13.0"
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-
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gem "
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-
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gem "yard", "~> 0.9"
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gem "bio"
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# gem "rake", "~> 13.0"
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# gem "minitest", "~> 5.0"
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# gem "yard", "~> 0.9"
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# gem "bio", "~> 2.0.0"
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data/README.md
CHANGED
@@ -1,10 +1,10 @@
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1
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[![Test](https://github.com/MizLab/Mizlab-ruby/actions/workflows/minitest.yml/badge.svg)](https://github.com/MizLab/Mizlab-ruby/actions/workflows/minitest.yml)
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[![Build page](https://github.com/MizLab/Mizlab-ruby/actions/workflows/yardoc.yml/badge.svg)](https://github.com/MizLab/Mizlab-ruby/actions/workflows/yardoc.yml)
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[![Gem Version](https://badge.fury.io/rb/mizlab.svg)](https://badge.fury.io/rb/mizlab)
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# Mizlab-ruby
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This gem is for easy handling of the processes used in our
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This gem is for easy handling of the processes used in our laboratory.
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## Installation
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@@ -14,7 +14,7 @@ Install it yourself as:
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gem install mizlab
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```
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-
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Or add below to your application's Gemfile:
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```ruby
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gem 'mizlab'
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@@ -38,7 +38,7 @@ To install this gem onto your local machine, run `bundle exec rake install`. To
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## Contributing
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Bug reports and pull requests are welcome on GitHub at https://github.com/
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Bug reports and pull requests are welcome on GitHub at https://github.com/MizLab/Mizlab-ruby
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## License
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data/lib/mizlab/version.rb
CHANGED
data/lib/mizlab.rb
CHANGED
@@ -4,6 +4,7 @@ require_relative "mizlab/version"
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4
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require "set"
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require "bio"
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require "stringio"
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require "rexml/document"
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module Mizlab
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class << self
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@@ -138,6 +139,23 @@ module Mizlab
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return local_pattern_list
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end
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# Fetch Taxonomy information from Taxonomy ID. can be give block too.
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# @param [String/Integer] taxonid Taxonomy ID, or Array of its.
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# @return [Hash] Taxonomy informations.
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# @yield [Hash] Taxonomy informations.
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def fetch_taxon(taxonid)
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taxonid = taxonid.is_a?(Array) ? taxonid : [taxonid]
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taxonid.each do |id|
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obj = Bio::NCBI::REST::EFetch.taxonomy(id, "xml")
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hashed = xml_to_hash(REXML::Document.new(obj).root)
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if block_given?
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yield hashed[:TaxaSet][:Taxon][:LineageEx][:Taxon]
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else
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return hashed[:TaxaSet][:Taxon][:LineageEx][:Taxon]
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end
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end
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end
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private
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def fetch_protein(accession)
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@@ -243,5 +261,21 @@ module Mizlab
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yield e
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end
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end
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# Convert XML to Hash.
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# @param [REXML::Document] element XML object.
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# @return [Hash] Hash that converted from xml.
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def xml_to_hash(element)
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value = (if element.has_elements?
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children = {}
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element.each_element do |e|
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children.merge!(xml_to_hash(e)) { |k, v1, v2| v1.is_a?(Array) ? v1 << v2 : [v1, v2] }
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end
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children
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else
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element.text
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end)
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return { element.name.to_sym => value }
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end
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end
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end
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data/mizlab.gemspec
CHANGED
@@ -29,8 +29,14 @@ Gem::Specification.new do |spec|
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spec.executables = spec.files.grep(%r{\Aexe/}) { |f| File.basename(f) }
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spec.require_paths = ["lib"]
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#
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-
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# Dependency
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spec.add_dependency "bio", "~> 2.0.0"
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spec.add_dependency "rexml", ">= 0"
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# Dependency (for development)
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spec.add_development_dependency "rake", "~> 13.0"
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spec.add_development_dependency "yard", "~> 0.9"
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spec.add_development_dependency "minitest", "~> 5.0"
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# For more information and examples about making a new gem, checkout our
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# guide at: https://bundler.io/guides/creating_gem.html
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metadata
CHANGED
@@ -1,15 +1,85 @@
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--- !ruby/object:Gem::Specification
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name: mizlab
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version: !ruby/object:Gem::Version
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version: 0.1.
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version: 0.1.6
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platform: ruby
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authors:
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- Omochice
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autorequire:
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bindir: exe
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cert_chain: []
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-
date: 2021-10-
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dependencies:
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date: 2021-10-28 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bio
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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: 2.0.0
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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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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: 2.0.0
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- !ruby/object:Gem::Dependency
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name: rexml
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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: :runtime
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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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- !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: '13.0'
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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: '13.0'
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- !ruby/object:Gem::Dependency
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name: yard
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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: '0.9'
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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: '0.9'
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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: '5.0'
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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: '5.0'
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description: The tools for our laboratory
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email:
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- mochice.mls.ntl@gmail.com
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