bio-twobit 0.1.4 → 0.2.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 1f0ce7759c6099bf6f2675eb467722473f06040a583cad13f2400c1d50f4f3b7
-  data.tar.gz: '09bdb93292cc70fa665a73890d8500b56084639cc3e18d6a1602bdf62d943620'
+  metadata.gz: 54ca968d6522ecade29dea715e43dda98eff1c2ea8fff65f446dd5e5ea19b357
+  data.tar.gz: 76def4a53e2df05f421a927334bb4441de477ca77409b0e37bbd99bda79ac657
 SHA512:
-  metadata.gz: ec2fb805c335562a64eca155c5806f3d004b8c4d3a2f6c2363eeb0c529749bb3f220bea4cf626d8d1618d6bdd061b247ae5a50a3f6d94314fbf6d0752bed281e
-  data.tar.gz: 96784953366c86e9e8e3d215a809faf0f23e6f012d3ff158ad47e80651fa2bea8cd0f87a3ca630579f7bb8e1aa41c2a30e449ba8af612ab8921d62e41521d293
+  metadata.gz: ed21093a59367927ce28bc45ddba7bad0bc0d497e3516f41de9a6cc127d510a562a621ad892db9946894c48124c142cc05fcd9861adc25c649a9d32336438245
+  data.tar.gz: f0091bf42601a641c49a1de4751fc2c79f1c2059db50e2891a34738700dbc6166deaf46e0f8f16a95b506fdaf60eb2e2e2a035e1258c34c99cb4e4027f67ffc2

data/LICENSE.txt

@@ -19,3 +19,14 @@ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 THE SOFTWARE.
+
+Code from red-datasets is used for automatic file download and caching
+https://github.com/red-data-tools/red-datasets
+
+Copyright 2017 Kouhei Sutou <kou@clear-code.com>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

@@ -13,6 +13,9 @@ Ruby bindings to [lib2bit](https://github.com/dpryan79/lib2bit) / [py2bit](https
 gem install bio-twobit
 ```
 
+Linux and macOS are supported.
+Windows is currently not supported.
+
 ## Usage
 
 Downlaod BSgenome.Hsapiens.UCSC.hg38
@@ -21,7 +24,7 @@ Downlaod BSgenome.Hsapiens.UCSC.hg38
 wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit
 ```
 
-Quick Start
+### Quick Start
 
 ```ruby
 require 'bio/twobit'
@@ -44,10 +47,19 @@ hg38.chroms.take(5)
 # ["chr3", 198295559],
 # ["chr4", 190214555],
 # ["chr5", 181538259]]
+```
+
+Fetch a sequence
 
+```ruby
 hg38.sequence("chr1", 50000, 50050)
-# "AAACAGGTTAATCGCCACGACATAGTAGTATTTAGAGTTACTAGTAAGCC"
+# "AAACAGGTTAATCGCCACGACATAGTAGTATTTAGAGTTACTAGTAAGCC" # length 50
+```
 
+* The first number is the **(0-based)** position on the chromosome/contig where the sequence should begin. 
+* The second number is the **(1-based)** position on the chromosome where the sequence should end.
+
+```ruby
 hg38.bases("chr1", 10000, 10100)
 # {"A"=>0.34, "C"=>0.49, "T"=>0.17, "G"=>0.0}
 
@@ -64,7 +76,7 @@ hg38.hard_masked_blocks("chr1", 0, 1000000)
 # [[0, 10000], [207666, 257666], [297968, 347968], [535988, 585988]]
 ```
 
-The 2-bit file must be closed explicitly. Alternatively, you can use a block. (If you forget to close the file, it will probably be closed by GC).
+The 2-bit file must be closed explicitly. Alternatively, you can use a block. Even if it is not closed, it will probably be closed by GC and there will be no problem. But this is not guaranteed.
 
 ```ruby
 # Explicitly close the file.
@@ -81,7 +93,7 @@ end
 tb.closed? # true / false
 ```
 
-If you would like to include information about soft-masked bases, you need to manually specify `masked: true`
+If you would like to include information about soft-masked bases, you need to specify `masked: true`
 
 ```ruby
 tb = Bio::TwoBit.open("test/fixtures/foo.2bit")
@@ -99,6 +111,29 @@ tb.soft_masked_blocks("chr1")
 tb.masked? # true / false
 ```
 
+## hg19, hg38, hs1...
+
+Some reference genomes are provided as classes in advance. These classes automatically download 2bit files from the UCSC site into a cache directory upon first use.
+
+```ruby
+hg19 = Bio::TwoBit::Hg19.new
+hg38 = Bio::TwoBit::Hg38.new
+hs1  = Bio::TwoBit::Hs1.new
+```
+
+Adding a new reference genome is easy. Add [here](https://github.com/ruby-on-bioc/bio-twobit/blob/main/lib/bio/twobit/references/template.erb) the id of the genome you want to use. 
+
+```
+git clone https://github.com/ruby-on-bioc/bio-twobit
+vi lib/bio/twobit/references/template.erb # Add your id to ids list.
+ruby lib/bio/twobit/references/template.erb
+rake install
+```
+
+If you want to use 2-bit files from locations other than UCSC, create your own classes [here](https://github.com/ruby-on-bioc/bio-twobit/tree/main/lib/bio/twobit/references).
+
+Pull requests are welcome.
+
 ## Development
 
 Bug reports and pull requests are welcome on GitHub at https://github.com/ruby-on-bioc/bio-twobit.
@@ -110,3 +145,6 @@ Bug reports and pull requests are welcome on GitHub at https://github.com/ruby-o
 ## License
 
 The gem is available as open source under the terms of the [MIT License](https://opensource.org/licenses/MIT).
+
+Code from [Red Datasets](https://github.com/red-data-tools/red-datasets) is used for automatic file download and caching. (The MIT license)
+

data/lib/bio/twobit/cache_path.rb

@@ -0,0 +1,32 @@
+# https://github.com/red-data-tools/red-datasets/blob/master/lib/datasets/cache-path.rb
+
+module Bio
+  class TwoBit
+    class CachePath
+      def initialize(id)
+        @id = id
+      end
+
+      def base_dir
+        Pathname(system_cache_dir).expand_path + "bio-twobit" + @id
+      end
+
+      def remove
+        FileUtils.rmtree(base_dir.to_s, secure: true) if base_dir.exist?
+      end
+
+      private
+
+      def system_cache_dir
+        case RUBY_PLATFORM
+        when /mswin/, /mingw/
+          ENV["LOCALAPPDATA"] || "~/AppData/Local"
+        when /darwin/
+          "~/Library/Caches"
+        else
+          ENV["XDG_CACHE_HOME"] || "~/.cache"
+        end
+      end
+    end
+  end
+end

data/lib/bio/twobit/downloader.rb

@@ -0,0 +1,282 @@
+# https://github.com/red-data-tools/red-datasets/blob/master/lib/datasets/downloader.rb
+
+require "fileutils"
+begin
+  require "io/console"
+rescue LoadError
+end
+require "net/http"
+require "pathname"
+
+module Bio
+  class TwoBit
+    class Downloader
+      class TooManyRedirects < StandardError; end
+
+      def initialize(url)
+        url = if url.is_a?(URI::Generic)
+                url.dup
+              else
+                URI.parse(url)
+              end
+        @url = url
+        return if @url.is_a?(URI::HTTP)
+
+        raise ArgumentError, "download URL must be HTTP or HTTPS: <#{@url}>"
+      end
+
+      def download(output_path)
+        return if output_path.exist?
+
+        output_path.parent.mkpath
+
+        headers = {
+          "Accept-Encoding" => "identity",
+          "User-Agent" => "BioTwobit/#{VERSION}"
+        }
+        start = nil
+        partial_output_path = Pathname.new("#{output_path}.partial")
+        if partial_output_path.exist?
+          start = partial_output_path.size
+          headers["Range"] = "bytes=#{start}-"
+        end
+
+        start_http(@url, headers) do |response|
+          if response.is_a?(Net::HTTPPartialContent)
+            mode = "ab"
+          else
+            start = nil
+            mode = "wb"
+          end
+
+          base_name = @url.path.split("/").last
+          size_current = 0
+          size_max = response.content_length
+          if start
+            size_current += start
+            size_max += start
+          end
+          progress_reporter = ProgressReporter.new(base_name, size_max)
+          partial_output_path.open(mode) do |output|
+            response.read_body do |chunk|
+              size_current += chunk.bytesize
+              progress_reporter.report(size_current)
+              output.write(chunk)
+            end
+          end
+        end
+        FileUtils.mv(partial_output_path, output_path)
+      rescue TooManyRedirects => e
+        last_url = e.message[/\Atoo many redirections: (.+)\z/, 1]
+        raise TooManyRedirects, "too many redirections: #{@url} .. #{last_url}"
+      end
+
+      private def start_http(url, headers, limit = 10, &block)
+        raise TooManyRedirects, "too many redirections: #{url}" if limit == 0
+
+        http = Net::HTTP.new(url.hostname, url.port)
+        # http.set_debug_output($stderr)
+        http.use_ssl = (url.scheme == "https")
+        http.start do
+          path = url.path
+          path += "?#{url.query}" if url.query
+          request = Net::HTTP::Get.new(path, headers)
+          http.request(request) do |response|
+            case response
+            when Net::HTTPSuccess, Net::HTTPPartialContent
+              return block.call(response)
+            when Net::HTTPRedirection
+              url = URI.parse(response[:location])
+              warn "Redirect to #{url}"
+              return start_http(url, headers, limit - 1, &block)
+            else
+              message = response.code
+              message += ": #{response.message}" if response.message and !response.message.empty?
+              message += ": #{url}"
+              raise response.error_type.new(message, response)
+            end
+          end
+        end
+      end
+
+      class ProgressReporter
+        def initialize(base_name, size_max)
+          @base_name = base_name
+          @size_max = size_max
+
+          @time_previous = Time.now
+          @size_previous = 0
+
+          @need_report = ($stderr == STDERR and $stderr.tty?)
+        end
+
+        def report(size_current)
+          return unless @need_report
+          return if @size_max.nil?
+          return unless foreground?
+
+          done = (size_current == @size_max)
+          time_current = Time.now
+          return if !done and time_current - @time_previous <= 1
+
+          read_bytes = size_current - @size_previous
+          throughput = read_bytes.to_f / (time_current - @time_previous)
+          @time_previous = time_current
+          @size_previous = size_current
+
+          message = build_message(size_current, throughput)
+          $stderr.print("\r#{message}") if message
+          $stderr.puts if done
+        end
+
+        private
+
+        def build_message(size_current, throughput)
+          percent = (size_current / @size_max.to_f) * 100
+          formatted_size = format("[%s/%s]", format_size(size_current), format_size(@size_max))
+          rest_second = (@size_max - size_current) / throughput
+          separator = " - "
+          progress = format("%05.1f%% %s %s %s", percent, formatted_size, format_time_interval(rest_second),
+                            format_throughput(throughput))
+          base_name = @base_name
+
+          width = guess_terminal_width
+          return "#{base_name}#{separator}#{progress}" if width.nil?
+
+          return nil if progress.size > width
+
+          base_name_width = width - progress.size - separator.size
+          if base_name.size > base_name_width
+            ellipsis = "..."
+            shorten_base_name_width = base_name_width - ellipsis.size
+            return progress if shorten_base_name_width < 1
+
+            base_name = base_name[0, shorten_base_name_width] + ellipsis
+
+          end
+          "#{base_name}#{separator}#{progress}"
+        end
+
+        def format_size(size)
+          if size < 1000
+            "%d" % size
+          elsif size < (1000**2)
+            format("%6.2fKB", (size.to_f / 1000))
+          elsif size < (1000**3)
+            format("%6.2fMB", (size.to_f / (1000**2)))
+          elsif size < (1000**4)
+            format("%6.2fGB", (size.to_f / (1000**3)))
+          else
+            format("%.2fTB", (size.to_f / (1000**4)))
+          end
+        end
+
+        def format_time_interval(interval)
+          if interval < 60
+            "00:00:%02d" % interval
+          elsif interval < (60 * 60)
+            minute, second = interval.divmod(60)
+            format("00:%02d:%02d", minute, second)
+          elsif interval < (60 * 60 * 24)
+            minute, second = interval.divmod(60)
+            hour, minute = minute.divmod(60)
+            format("%02d:%02d:%02d", hour, minute, second)
+          else
+            minute, second = interval.divmod(60)
+            hour, minute = minute.divmod(60)
+            day, hour = hour.divmod(24)
+            format("%dd %02d:%02d:%02d", day, hour, minute, second)
+          end
+        end
+
+        def format_throughput(throughput)
+          throughput_byte = throughput / 8
+          if throughput_byte <= 1000
+            "%3dB/s" % throughput_byte
+          elsif throughput_byte <= (1000**2)
+            format("%3dKB/s", (throughput_byte / 1000))
+          elsif throughput_byte <= (1000**3)
+            format("%3dMB/s", (throughput_byte / (1000**2)))
+          else
+            format("%3dGB/s", (throughput_byte / (1000**3)))
+          end
+        end
+
+        def foreground?
+          proc_stat_path = "/proc/self/stat"
+          ps_path = "/bin/ps"
+
+          if File.exist?(proc_stat_path)
+            stat = File.read(proc_stat_path).sub(/\A.+\) /, "").split
+            process_group_id = stat[2]
+            terminal_process_group_id = stat[5]
+            process_group_id == terminal_process_group_id
+          elsif File.executable?(ps_path)
+            IO.pipe do |input, output|
+              pid = spawn(ps_path, "-o", "stat", "-p", Process.pid.to_s,
+                          { out: output, err: output })
+              output.close
+              _, status = Process.waitpid2(pid)
+              return false unless status.success?
+
+              input.each_line.to_a.last.include?("+")
+            end
+          else
+            false
+          end
+        end
+
+        def guess_terminal_width
+          guess_terminal_width_from_io ||
+            guess_terminal_width_from_command ||
+            guess_terminal_width_from_env ||
+            80
+        end
+
+        def guess_terminal_width_from_io
+          if IO.respond_to?(:console)
+            IO.console.winsize[1]
+          elsif $stderr.respond_to?(:winsize)
+            begin
+              $stderr.winsize[1]
+            rescue SystemCallError
+              nil
+            end
+          end
+        end
+
+        def guess_terminal_width_from_command
+          IO.pipe do |input, output|
+            begin
+              pid = spawn("tput", "cols", { out: output, err: output })
+            rescue SystemCallError
+              return nil
+            end
+
+            output.close
+            _, status = Process.waitpid2(pid)
+            return nil unless status.success?
+
+            result = input.read.chomp
+            begin
+              Integer(result, 10)
+            rescue ArgumentError
+              nil
+            end
+          end
+        end
+
+        def guess_terminal_width_from_env
+          env = ENV["COLUMNS"] || ENV["TERM_WIDTH"]
+          return nil if env.nil?
+
+          begin
+            Integer(env, 10)
+          rescue ArgumentError
+            nil
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bio/twobit/metadata.rb

@@ -0,0 +1,9 @@
+module Bio
+  class TwoBit
+    class Metadata < Struct.new(:id,
+                                :name,
+                                :url,
+                                :description)
+    end
+  end
+end

data/lib/bio/twobit/reference_genome.rb

@@ -0,0 +1,24 @@
+module Bio
+  class TwoBit
+    class ReferenceGenome < TwoBit
+      def self.open(*args, **kwargs, &block)
+        raise ArgumentError, "#{self}#open() does not accept arguments" if args.any?
+
+        super(**kwargs, &block)
+      end
+
+      def initialize(**kwargs)
+        @local_name ||= File.basename(@data_url)
+        super(prepare_data, **kwargs)
+      end
+
+      private
+
+      def prepare_data
+        data_path = cache_dir_path + @local_name
+        download(data_path, @data_url)
+        data_path
+      end
+    end
+  end
+end

data/lib/bio/twobit/references/danrer10.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class DanRer10 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "danRer10"
+        @metadata.name = "danRer10"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/danRer10/bigZips/danRer10.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

data/lib/bio/twobit/references/danrer11.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class DanRer11 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "danRer11"
+        @metadata.name = "danRer11"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/danRer11/bigZips/danRer11.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

data/lib/bio/twobit/references/dm6.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class Dm6 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "dm6"
+        @metadata.name = "dm6"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/dm6/bigZips/dm6.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

data/lib/bio/twobit/references/hg19.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class Hg19 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "hg19"
+        @metadata.name = "hg19"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

data/lib/bio/twobit/references/hg38.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class Hg38 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "hg38"
+        @metadata.name = "hg38"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

data/lib/bio/twobit/references/hs1.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class Hs1 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "hs1"
+        @metadata.name = "hs1"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/hs1/bigZips/hs1.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

data/lib/bio/twobit/references/mm10.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class Mm10 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "mm10"
+        @metadata.name = "mm10"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/mm10.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

data/lib/bio/twobit/references/mm39.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class Mm39 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "mm39"
+        @metadata.name = "mm39"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/mm39.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

data/lib/bio/twobit/references/mm9.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class Mm9 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "mm9"
+        @metadata.name = "mm9"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/mm9/bigZips/mm9.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

data/lib/bio/twobit/version.rb

@@ -2,6 +2,6 @@
 
 module Bio
   class TwoBit
-    VERSION = "0.1.4"
+    VERSION = "0.2.0"
   end
 end

data/lib/bio/twobit.rb

@@ -1,26 +1,51 @@
 # frozen_string_literal: true
 
+require "pathname"
 require_relative "twobit/version"
 require_relative "twobit/twobit"
+require_relative "twobit/cache_path"
+require_relative "twobit/downloader"
+require_relative "twobit/metadata"
 
 module Bio
   # Reader for .2bit files (i.e., from UCSC genome browser)
   class TwoBit
-    def self.open(*args, **kwargs)
-      file = new(*args, **kwargs)
-      return file unless block_given?
-
-      begin
-        yield file
-      ensure
-        file.close
+    attr_reader :metadata
+
+    class << self
+      def open(*args, **kwargs)
+        file = new(*args, **kwargs)
+        return file unless block_given?
+
+        begin
+          yield file
+        ensure
+          file.close
+        end
+        file
+      end
+
+      # Here, const_missing is used instead of autoload.
+
+      def const_missing(name)
+        # prevents const_get from being called recursively many times.
+        @missing_const ||= []
+        super if @missing_const.include? name
+        @missing_const << name
+
+        path = File.join(__dir__, "twobit/references", "#{name.to_s.downcase}.rb")
+        if File.exist?(path)
+          require path
+          return const_get(name)
+        end
+        super
       end
-      file
     end
 
     def initialize(fname, masked: false)
       raise "TwoBit::new() does not take block; use TwoBit::open() instead" if block_given?
 
+      fname = fname.to_path if fname.respond_to?(:to_path)
       @fname = fname
       if masked
         mskd = 1
@@ -49,6 +74,8 @@ module Bio
       sequence_raw(chrom, start, stop)
     end
 
+    alias seq sequence
+
     def bases(chrom, start = 0, stop = 0, fraction: true)
       raise ArgumentError, "negative start position" if start.negative?
       raise ArgumentError, "negative stop position" if stop.negative?
@@ -69,5 +96,24 @@ module Bio
 
       soft_masked_blocks_raw(chrom, start, stop)
     end
+
+    def clear_cache!
+      cache_path.remove
+    end
+
+    private
+
+    def cache_dir_path
+      cache_path.base_dir
+    end
+
+    def cache_path
+      @cache_path ||= CachePath.new(@metadata.id)
+    end
+
+    def download(output_path, url)
+      downloader = Downloader.new(url)
+      downloader.download(output_path)
+    end
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-twobit
 version: !ruby/object:Gem::Version
-  version: 0.1.4
+  version: 0.2.0
 platform: ruby
 authors:
 - kojix2
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-11-03 00:00:00.000000000 Z
+date: 2023-01-11 00:00:00.000000000 Z
 dependencies: []
 description: This is a Ruby binding for lib2bit(https://github.com/dpryan79/lib2bit),
   which provides high-speed access to genomic data in 2bit file format.
@@ -19,12 +19,8 @@ extensions:
 - ext/bio/twobit/extconf.rb
 extra_rdoc_files: []
 files:
-- ".rubocop.yml"
-- Gemfile
 - LICENSE.txt
 - README.md
-- Rakefile
-- bio-twobit.gemspec
 - ext/bio/twobit/2bit.c
 - ext/bio/twobit/2bit.h
 - ext/bio/twobit/LICENSE
@@ -32,6 +28,19 @@ files:
 - ext/bio/twobit/twobit.c
 - ext/bio/twobit/twobit.h
 - lib/bio/twobit.rb
+- lib/bio/twobit/cache_path.rb
+- lib/bio/twobit/downloader.rb
+- lib/bio/twobit/metadata.rb
+- lib/bio/twobit/reference_genome.rb
+- lib/bio/twobit/references/danrer10.rb
+- lib/bio/twobit/references/danrer11.rb
+- lib/bio/twobit/references/dm6.rb
+- lib/bio/twobit/references/hg19.rb
+- lib/bio/twobit/references/hg38.rb
+- lib/bio/twobit/references/hs1.rb
+- lib/bio/twobit/references/mm10.rb
+- lib/bio/twobit/references/mm39.rb
+- lib/bio/twobit/references/mm9.rb
 - lib/bio/twobit/version.rb
 homepage: https://github.com/ruby-on-bioc/bio-twobit
 licenses:
@@ -52,7 +61,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.3.7
+rubygems_version: 3.4.1
 signing_key: 
 specification_version: 4
 summary: A ruby library for accessing 2bit files

data/.rubocop.yml

@@ -1,13 +0,0 @@
-AllCops:
-  TargetRubyVersion: 2.6
-
-Style/StringLiterals:
-  Enabled: true
-  EnforcedStyle: double_quotes
-
-Style/StringLiteralsInInterpolation:
-  Enabled: true
-  EnforcedStyle: double_quotes
-
-Layout/LineLength:
-  Max: 120

data/Gemfile

@@ -1,11 +0,0 @@
-# frozen_string_literal: true
-
-source "https://rubygems.org"
-
-# Specify your gem's dependencies in bio-twobit.gemspec
-gemspec
-
-gem "rake"
-gem "rake-compiler"
-gem "test-unit"
-gem "rubocop"

data/Rakefile

@@ -1,25 +0,0 @@
-# frozen_string_literal: true
-
-require "bundler/gem_tasks"
-require "rake/testtask"
-
-Rake::TestTask.new(:test) do |t|
-  t.libs << "test"
-  t.libs << "lib"
-  t.test_files = FileList["test/**/*_test.rb"]
-end
-
-require "rubocop/rake_task"
-
-RuboCop::RakeTask.new
-
-require "rake/extensiontask"
-
-task build: :compile
-
-Rake::ExtensionTask.new("twobit") do |ext|
-  ext.lib_dir = "lib/bio/twobit"
-  ext.ext_dir = "ext/bio/twobit"
-end
-
-task default: %i[clobber compile test]

data/bio-twobit.gemspec

@@ -1,25 +0,0 @@
-# frozen_string_literal: true
-
-require_relative "lib/bio/twobit/version"
-
-Gem::Specification.new do |spec|
-  spec.name          = "bio-twobit"
-  spec.version       = Bio::TwoBit::VERSION
-  spec.authors       = ["kojix2"]
-  spec.email         = ["2xijok@gmail.com"]
-
-  spec.summary       = "A ruby library for accessing 2bit files"
-  spec.description   = "This is a Ruby binding for lib2bit(https://github.com/dpryan79/lib2bit), " \
-                       "which provides high-speed access to genomic data in 2bit file format."
-  spec.homepage      = "https://github.com/ruby-on-bioc/bio-twobit"
-  spec.license       = "MIT"
-  spec.required_ruby_version = ">= 2.6.0"
-
-  spec.files = Dir.chdir(File.expand_path(__dir__)) do
-    `git ls-files -z`.split("\x0").reject do |f|
-      (f == __FILE__) || f.match(%r{\A(?:(?:test|spec|features)/|\.(?:git|travis|circleci)|appveyor)})
-    end
-  end
-  spec.require_paths = ["lib"]
-  spec.extensions    = ["ext/bio/twobit/extconf.rb"]
-end