mizlab 0.1.4 → 0.1.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 66e83019b3716a3b8bdb55bd6d14df9764821fe394547f3d54e34f26ca5bab06
-  data.tar.gz: 794444eaeff6a46f8e3cddc1e6173b746df7eab24a7b1fd1454dac8c4e4bc79d
+  metadata.gz: 4407f6c76b786fe0c6bdc8a70ef04bbbd721bf247cf9d96de66be8300e137dbe
+  data.tar.gz: f404ba612019c0f19f28f7da7d660c31c7eb2a53bba962f1e495be25a19fe52e
 SHA512:
-  metadata.gz: 9bd7ab8e6be7264a6ba6a392685a271755320c555a459b1554797577f57ab387ce5e45762cd20341fa6749dc9117f4ac216d1a62d388d8386e2fd7b17a526761
-  data.tar.gz: fa475f06c3d361eff8bd3c19787e26ec973daca6a73e66f6bdccb414e4ddba5abe10a544ca2eb002f9c26eee6c532b4dbb964ea6eac6a66fa9f28a4ef69a2514
+  metadata.gz: adbe76a35b85afff62667f50be8913936486ad9928edb51d9ded44ab20b4c9c30ecb3a106f8b92474c998d55630d85aeebe40aa678a2c4ec0ef81c887480c181
+  data.tar.gz: dee0b71988bb5b80103984d9f81b8cba8156d3ebce89728a423ee9e3517011444e4ac1ef13cd692ebb88caa3f1f2d8e6f44e839e5a812100211ba5326014d801

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 = "0.1.4"
+  VERSION = "0.1.5"
 end

data/lib/mizlab.rb

@@ -7,22 +7,63 @@ require "stringio"
 
 module Mizlab
   class << self
+    # 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 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 getobj(accessions, is_protein = false)
-      accessions = accessions.is_a?(String) ? [accessions] : accessions
-      accessions.each do |acc|
-        ret = is_protein ? fetch_protein(acc) : fetch_nucleotide(acc)
-        parse(ret) do |o|
+      getent(accessions, is_protein) do |entry|
+        parse(entry) do |o|
           if block_given?
             yield o
           else
             return o
           end
         end
-        sleep(0.37) # Using 0.333... seconds, sometimes hit the NCBI rate limit
+      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
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: mizlab
 version: !ruby/object:Gem::Version
-  version: 0.1.4
+  version: 0.1.5
 platform: ruby
 authors:
 - Omochice