mizlab 0.1.0 → 0.1.6

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: aaac55320663e3b8fef03c5518d73156ea3a1880736936c8debb1a6eb9d60935
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data/.github/workflows/deploy.yml

@@ -18,4 +18,4 @@ jobs:
           # Optional, will publish to RubyGems if specified
           api_key: ${{secrets.RUBYGEMS_API_KEY}}
           # Optional, will publish to GitHub Packages if specified
-          github_token: ${{secrets.GITHUB_TOKEN}}
+          # github_token: ${{secrets.GITHUB_TOKEN}}

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/Rakefile

@@ -16,4 +16,24 @@ YARD::Rake::YardocTask.new do |t|
   t.stats_options = ["--list-undoc"]
 end
 
+desc "Version up"
+task :versionup do
+  version = ""
+  File.open("./lib/mizlab/version.rb") do |f|
+    version = f.read[(/(\d+\.\d+\.\d+)/)]
+  end
+  ver, minor_ver, hotfix = version.split(".")
+  hotfix = hotfix.to_i + 1
+  new_version = "#{ver}.#{minor_ver}.#{hotfix}"
+  cmd = "sed -E -i 's/[0-9]+\\.[0-9]+\\.[0-9]+/#{new_version}/' ./lib/mizlab/version.rb"
+  puts(cmd)
+  system(cmd)
+  cmd = "git add ./lib/mizlab/version.rb && git commit -m ':rocket: Version up'"
+  puts(cmd)
+  system(cmd)
+  cmd = "git tag v#{new_version}"
+  puts(cmd)
+  system(cmd)
+end
+
 task default: :test

data/lib/mizlab/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Mizlab
-  VERSION = "0.1.0"
+  VERSION = "0.1.6"
 end

data/lib/mizlab.rb

@@ -3,28 +3,68 @@
 require_relative "mizlab/version"
 require "set"
 require "bio"
+require "stringio"
+require "rexml/document"
 
 module Mizlab
   class << self
-    # Fetch data via genbank
-    # @param  [String] accession Accession number Like "NC_012920".
-    # @param  [Bool] is_protein wheather the accession is protein. Default to true.
-    # @return [Bio::GenBank] GenBank object.
-    def getobj(accession, is_protein = false)
-      ret = is_protein ? fetch_protein(accession) : fetch_nucleotide(accession)
-      parse(ret) do |o|
-        return o
+    # Get entry as String. You can also give a block.
+    # @param  [String/Array] accessions Accession numbers like ["NC_012920", ...].
+    # @return [String] Entry as string.
+    # @yield  [String] Entry as string.
+    def getent(accessions, is_protein = false)
+      accessions = accessions.is_a?(String) ? [accessions] : accessions
+      accessions.each do |acc|
+        ret = is_protein ? fetch_protein(acc) : fetch_nucleotide(acc)
+        if block_given?
+          yield ret
+        else
+          return ret
+        end
+        sleep(0.37) # Using 0.333... seconds, sometimes hit the NCBI rate limit
       end
     end
 
-    # Fetch multiple data via genbank
-    # @param  [Array] accessions Array of accession string.
+    # Fetch data via genbank. You can also give a block.
+    # @param  [String/Array] accessions Accession numbers Like ["NC_012920", ...].
     # @param  [Bool] is_protein wheather the accession is protein. Default to true.
+    # @return [Bio::GenBank] GenBank object.
     # @yield  [Bio::GenBank] GenBank object.
-    def getobjs(accessions, is_protein = false)
-      ret = is_protein ? fetch_protein(accessions) : fetch_nucleotide(accessions)
-      parse(ret) do |o|
-        yield o
+    def getobj(accessions, is_protein = false)
+      getent(accessions, is_protein) do |entry|
+        parse(entry) do |o|
+          if block_given?
+            yield o
+          else
+            return o
+          end
+        end
+      end
+    end
+
+    # Save object.
+    # @param  [String] filename Filepath from executed source.
+    # @param  [Bio::DB] obj Object which inherits from `Bio::DB`.
+    # @return [nil]
+    def savefile(filename, obj)
+      if File.exists?(filename)
+        yes = Set.new(["N", "n", "no"])
+        no = Set.new(["Y", "y", "yes"])
+        loop do
+          print("#{filename} exists already. Overwrite? [y/n] ")
+          inputed = gets.rstrip
+          if yes.include?(inputed)
+            return
+          elsif no.include?(inputed)
+            break
+          end
+          puts("You should input 'y' or 'n'")
+        end
+      end
+      File.open(filename, "w") do |f|
+        obj.tags.each do |t|
+          f.puts(obj.get(t))
+        end
       end
     end
 
@@ -99,6 +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)
@@ -106,7 +163,7 @@ module Mizlab
     end
 
     def fetch_nucleotide(accession)
-      return Bio::NCBI::REST::EFetch.protein(accession)
+      return Bio::NCBI::REST::EFetch.nucleotide(accession)
     end
 
     # get patterns from filled pixs.
@@ -200,14 +257,25 @@ module Mizlab
     # @param  [String] entries Entries as string
     # @yield  [Object] Object that match entry format.
     def parse(entries)
-      tmp_file_name = ".mizlab_fetch_tmpfile"
-      File.open(tmp_file_name, "w") do |f|
-        f.puts entries
-      end
-      Bio::FlatFile.auto(tmp_file_name).each_entry do |e|
+      Bio::FlatFile.auto(StringIO.new(entries)).each_entry do |e|
         yield e
       end
-      File.delete(tmp_file_name)
+    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: 0.1.0
+  version: 0.1.6
 platform: ruby
 authors:
 - Omochice
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2021-10-22 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