dna 0.0.11 → 0.0.12

data/Gemfile

@@ -1,2 +1,3 @@
 source :rubygems
 gem 'rspec'
+gem 'jeweler'

data/Rakefile

@@ -0,0 +1,48 @@
+# encoding: utf-8
+
+require 'rubygems'
+require 'bundler'
+
+DNA_VERSION = '0.0.12'
+
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  gem.name = "dna"
+  gem.homepage = "http://audy.github.com/dna"
+  gem.license = "MIT"
+  gem.summary = "Simple FASTA/FASTQ/QSEQ parser library for Ruby"
+  gem.description = "Simple FASTA/FASTQ/QSEQ parser library for Ruby."
+  gem.email = "harekrishna@gmail.com"
+  gem.authors = ["Austin G. Davis-Richardson"]
+  gem.version = DNA_VERSION
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+task :default => :test
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+
+  version = DNA_VERSION
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "test #{version}"
+  rdoc.rdoc_files.include('readme.md')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/dna.gemspec

@@ -1,19 +1,60 @@
-Gem::Specification.new do |s|
-	s.name    = 'dna'
-	s.version = '0.0.11'
-	s.date    = '2012-05-21'
-
-	s.summary     = 'DNA sequence parser'
-	s.description = 'for parsing various types of DNA sequence files'
+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
+# -*- encoding: utf-8 -*-
 
-	s.authors = ["Austin G. Davis-Richardson"]
-	s.email   = "harekrishna@gmail.com"
+Gem::Specification.new do |s|
+  s.name = "dna"
+  s.version = "0.0.12"
 
-	s.rubyforge_project = 'dna'
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["Austin G. Davis-Richardson"]
+  s.date = "2012-08-09"
+  s.description = "Simple FASTA/FASTQ/QSEQ parser library for Ruby."
+  s.email = "harekrishna@gmail.com"
+  s.executables = ["dna"]
+  s.files = [
+    ".rspec",
+    ".rvmrc",
+    "Gemfile",
+    "Rakefile",
+    "bin/dna",
+    "dna.gemspec",
+    "lib/dna.rb",
+    "lib/dna/dna.rb",
+    "lib/dna/parsers/fasta.rb",
+    "lib/dna/parsers/fastq.rb",
+    "lib/dna/parsers/qseq.rb",
+    "lib/dna/record.rb",
+    "readme.md",
+    "spec/data/empty.txt",
+    "spec/data/test.fasta",
+    "spec/data/test.fasta.gz",
+    "spec/data/test.fastq",
+    "spec/data/test.qseq",
+    "spec/dna_spec.rb",
+    "spec/record_spec.rb",
+    "spec/spec_helper.rb"
+  ]
+  s.homepage = "http://audy.github.com/dna"
+  s.licenses = ["MIT"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = "1.8.24"
+  s.summary = "Simple FASTA/FASTQ/QSEQ parser library for Ruby"
 
-	s.files         = `git ls-files`.split("\n")
-	s.test_files    = `git ls-files -- {test,spec,features}/*`.split("\n")
-  s.executables   = `git ls-files -- bin/*`.split("\n").map{ |f| File.basename(f) }
+  if s.respond_to? :specification_version then
+    s.specification_version = 3
 
-	s.homepage = "http://github.com/audy/dna"
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_runtime_dependency(%q<rspec>, [">= 0"])
+      s.add_runtime_dependency(%q<jeweler>, [">= 0"])
+    else
+      s.add_dependency(%q<rspec>, [">= 0"])
+      s.add_dependency(%q<jeweler>, [">= 0"])
+    end
+  else
+    s.add_dependency(%q<rspec>, [">= 0"])
+    s.add_dependency(%q<jeweler>, [">= 0"])
+  end
 end
+

data/lib/dna/dna.rb

@@ -0,0 +1,58 @@
+
+##
+# Dna
+#
+
+class Dna
+  include Enumerable
+
+  attr_reader :format
+
+  def initialize(handle)
+    @handle = handle
+    @format = detect_format
+    @iterator =
+      case @format
+      when :fasta
+        FastaParser.new @handle
+      when :fastq
+        FastqParser.new @handle
+      when :qseq
+        QSEQParser.new @handle
+      else
+        raise "#{@format} not supported."
+      end
+  end
+
+  def detect_format
+
+    # is gzipped?
+    unless @handle.class == Array # for tests mostly...
+      begin
+        @handle = Zlib::GzipReader.new(@handle)
+      rescue
+        @handle.rewind
+      end
+    end
+
+    first_line = @handle.first
+    @handle.rewind if @handle.class == File
+
+    return :unknown if first_line == nil
+
+    # detect qseq by counting number of tabs.
+    if first_line.split("\t").length == 11
+      return :qseq
+    elsif first_line[0].chr == '>'
+      return :fasta
+    elsif first_line[0].chr == '@'
+      return :fastq
+    else
+      raise Exception, "cannot detect format of input"
+    end
+  end
+
+  def each &block
+    @iterator.each(&block)
+  end
+end

data/lib/{parsers → dna/parsers}/fasta.rb

@@ -1,5 +1,5 @@
 class FastaParser
-  
+
   def initialize(handle)
     @handle = handle
   end
@@ -17,4 +17,20 @@ class FastaParser
     end
     yield Fasta.new(:name => header, :sequence => sequence)
   end
-end
+end
+
+##
+# Fasta record
+#
+class Fasta < Record
+  attr_accessor :name, :sequence
+
+  def initialize(args={})
+    @name = args[:name]
+    @sequence = args[:sequence]
+  end
+
+  def to_s
+    ">#{@name}\n#{@sequence}"
+  end
+end

data/lib/{parsers → dna/parsers}/fastq.rb

@@ -3,7 +3,7 @@ class FastqParser
   def initialize(handle)
     @handle = handle
   end
-  
+
   def each
     c = (0..3).cycle
     params = { :name => nil, :sequence => nil, :quality => nil }
@@ -23,4 +23,21 @@ class FastqParser
       end
     end
   end
-end
+end
+
+##
+# Fastq record
+#
+class Fastq < Record
+  attr_accessor :name, :sequence, :format, :quality
+
+  def initialize(args={})
+    @name = args[:name]
+    @sequence = args[:sequence]
+    @quality = args[:quality]
+  end
+
+  def to_s
+    "@#{@name}\n#{@sequence}\n+#{@name}\n#{@quality}"
+  end
+end

data/lib/dna/parsers/qseq.rb

@@ -0,0 +1,59 @@
+class QSEQParser
+
+  def initialize(handle)
+    @handle = handle
+  end
+
+  def each
+    @handle.each do |line|
+      line = line.strip.split("\t")
+      record = QSEQ.new(
+        :machine => line[0],
+        :run => line[1],
+        :lane => line[2],
+        :tile => line[3],
+        :x => line[4],
+        :y => line[5],
+        :index => line[6],
+        :read_no => line[7],
+        :sequence => line[8],
+        :quality => line[9],
+        :filtered => line[10]
+      )
+      yield record
+    end
+  end
+end
+
+##
+# QSEQ record
+#
+class QSEQ < Record
+
+  attr_accessor :machine, :run, :lane, :tile, :x, :y, :index, :read_no, :sequence, :quality, :filtered
+
+  def initialize(args={})
+    # These are the properties defined by the qseq spec
+    # they must be in the same order that they appear in the tab-separated qseq file
+    @properties = :machine, :run, :lane, :tile, :x, :y, :index, :read_no, :sequence, :quality, :filtered
+    @machine = args[:machine]
+    @run = args[:run]
+    @lane = args[:lane]
+    @tile = args[:tile]
+    @x = args[:x]
+    @y = args[:y]
+    @index = args[:index]
+    @read_no = args[:read_no]
+    @sequence = args[:sequence]
+    @quality = args[:quality]
+    @filtered = args[:filtered]
+  end
+
+  def to_s
+    @properties.collect { |x| self.send(x) }.join("\t")
+  end
+
+  def header
+    @properties.collect { |x| self.send(x) }.join("\t")
+  end
+end

data/lib/dna/record.rb

@@ -0,0 +1,7 @@
+class Record # nucleotide record
+  def length
+    @sequence.length
+  end
+end
+# load parsers after Record because they inherit from Record
+Dir.glob(File.join(File.dirname(__FILE__), 'parsers', '*.rb')).each { |f| require f }

data/lib/dna.rb

@@ -1,132 +1,3 @@
 require 'zlib'
 
-Dir.glob(File.join(File.dirname(__FILE__), 'parsers', '*.rb')).each { |f| require f }
-
-##
-# Dna
-#
-class Dna
-  include Enumerable
-
-  attr_reader :format
-
-  def initialize(handle)
-    @handle = handle
-    @format = detect_format
-    @iterator =
-      case @format
-      when :fasta
-        FastaParser.new @handle
-      when :fastq
-        FastqParser.new @handle
-      when :qseq
-        QSEQParser.new @handle
-      else
-        raise "#{@format} not supported."
-      end
-  end
-
-  def detect_format
-    
-    # is gzipped?
-    unless @handle.class == Array # for tests mostly...
-      begin
-        @handle = Zlib::GzipReader.new(@handle)
-      rescue
-        @handle.rewind
-      end
-    end
-    
-    first_line = @handle.first
-    @handle.rewind if @handle.class == File
-
-    return :unknown if first_line == nil
-
-    # detect qseq by counting number of tabs.
-    if first_line.split("\t").length == 11
-      return :qseq
-    elsif first_line[0].chr == '>'
-      return :fasta
-    elsif first_line[0].chr == '@'
-      return :fastq
-    else
-      raise Exception, "cannot detect format of input"
-    end
-  end
-
-  def each &block
-    @iterator.each(&block)
-  end
-end
-
-class Record # nucleotide record
-  def length
-    @sequence.length
-  end
-end
-
-##
-# Fasta record
-#
-class Fasta < Record
-  attr_accessor :name, :sequence
-
-  def initialize(args={})
-    @name = args[:name]
-    @sequence = args[:sequence]
-  end
-
-  def to_s
-    ">#{@name}\n#{@sequence}"
-  end
-end
-
-##
-# Fastq record
-#
-class Fastq < Record
-  attr_accessor :name, :sequence, :format, :quality
-
-  def initialize(args={})
-    @name = args[:name]
-    @sequence = args[:sequence]
-    @quality = args[:quality]
-  end
-
-  def to_s
-    "@#{@name}\n#{@sequence}\n+#{@name}\n#{@quality}"
-  end
-end
-
-##
-# QSEQ record
-#2
-class QSEQ < Record
-
-  attr_accessor :machine, :run, :lane, :tile, :x, :y, :index, :read_no, :sequence, :quality, :filtered
-
-  def initialize(args={})
-    # These are the properties defined by the qseq spec
-    # they must be in the same order that they appear in the tab-separated qseq file
-    @properties = :machine, :run, :lane, :tile, :x, :y, :index, :read_no, :sequence, :quality, :filtered
-    @machine = args[:machine]
-    @run = args[:run]
-    @lane = args[:lane]
-    @tile = args[:tile]
-    @x = args[:x]
-    @y = args[:y]
-    @index = args[:index]
-    @read_no = args[:read_no]
-    @sequence = args[:sequence]
-    @quality = args[:quality]
-    @filtered = args[:filtered]
-  end
-
-  def to_s
-    @properties.collect { |x| self.send(x) }.join("\t")
-  end
-
-  def header
-    @properties.collect { |x| self.send(x) }.join("\t")
-  end
-end
+Dir.glob(File.join(File.dirname(__FILE__), 'dna', '*.rb')).each { |f| require f }

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: dna
 version: !ruby/object:Gem::Version 
-  hash: 9
+  hash: 7
   prerelease: 
   segments: 
   - 0
   - 0
-  - 11
-  version: 0.0.11
+  - 12
+  version: 0.0.12
 platform: ruby
 authors: 
 - Austin G. Davis-Richardson
@@ -15,10 +15,37 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2012-05-21 00:00:00 Z
-dependencies: []
-
-description: for parsing various types of DNA sequence files
+date: 2012-08-09 00:00:00 Z
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  type: :runtime
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  version_requirements: *id001
+  name: rspec
+  prerelease: false
+- !ruby/object:Gem::Dependency 
+  type: :runtime
+  requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  version_requirements: *id002
+  name: jeweler
+  prerelease: false
+description: Simple FASTA/FASTQ/QSEQ parser library for Ruby.
 email: harekrishna@gmail.com
 executables: 
 - dna
@@ -30,12 +57,15 @@ files:
 - .rspec
 - .rvmrc
 - Gemfile
+- Rakefile
 - bin/dna
 - dna.gemspec
 - lib/dna.rb
-- lib/parsers/fasta.rb
-- lib/parsers/fastq.rb
-- lib/parsers/qseq.rb
+- lib/dna/dna.rb
+- lib/dna/parsers/fasta.rb
+- lib/dna/parsers/fastq.rb
+- lib/dna/parsers/qseq.rb
+- lib/dna/record.rb
 - readme.md
 - spec/data/empty.txt
 - spec/data/test.fasta
@@ -45,9 +75,9 @@ files:
 - spec/dna_spec.rb
 - spec/record_spec.rb
 - spec/spec_helper.rb
-homepage: http://github.com/audy/dna
-licenses: []
-
+homepage: http://audy.github.com/dna
+licenses: 
+- MIT
 post_install_message: 
 rdoc_options: []
 
@@ -73,17 +103,10 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: "0"
 requirements: []
 
-rubyforge_project: dna
+rubyforge_project: 
 rubygems_version: 1.8.24
 signing_key: 
 specification_version: 3
-summary: DNA sequence parser
-test_files: 
-- spec/data/empty.txt
-- spec/data/test.fasta
-- spec/data/test.fasta.gz
-- spec/data/test.fastq
-- spec/data/test.qseq
-- spec/dna_spec.rb
-- spec/record_spec.rb
-- spec/spec_helper.rb
+summary: Simple FASTA/FASTQ/QSEQ parser library for Ruby
+test_files: []
+

data/lib/parsers/qseq.rb

@@ -1,26 +0,0 @@
-class QSEQParser
-
-  def initialize(handle)
-    @handle = handle
-  end
-
-  def each
-    @handle.each do |line|
-      line = line.strip.split("\t")
-      record = QSEQ.new(
-        :machine => line[0],
-        :run => line[1],
-        :lane => line[2],
-        :tile => line[3],
-        :x => line[4],
-        :y => line[5],
-        :index => line[6],
-        :read_no => line[7],
-        :sequence => line[8],
-        :quality => line[9],
-        :filtered => line[10]
-      )
-      yield record
-    end
-  end
-end