scbi_fastq 0.0.18 → 0.0.19

data/test/solexa.fastq

@@ -0,0 +1,20 @@
+@SLXA-B3_649_FC8437_R1_1_1_610_79
+GATGTGCAATACCTTTGTAGAGGAA
++SLXA-B3_649_FC8437_R1_1_1_610_79
+YYYYYYYYYYYYYYYYYYWYWYYSU
+@SLXA-B3_649_FC8437_R1_1_1_397_389
+GGTTTGAGAAAGAGAAATGAGATAA
++SLXA-B3_649_FC8437_R1_1_1_397_389
+YYYYYYYYYWYYYYWWYYYWYWYWW
+@SLXA-B3_649_FC8437_R1_1_1_850_123
+GAGGGTGTTGATCATGATGATGGCG
++SLXA-B3_649_FC8437_R1_1_1_850_123
+YYYYYYYYYYYYYWYYWYYSYYYSY
+@SLXA-B3_649_FC8437_R1_1_1_362_549
+GGAAACAAAGTTTTTCTCAACATAG
++SLXA-B3_649_FC8437_R1_1_1_362_549
+YYYYYYYYYYYYYYYYYYWWWWYWY
+@SLXA-B3_649_FC8437_R1_1_1_183_714
+GTATTATTTAATGGCATACACTCAA
++SLXA-B3_649_FC8437_R1_1_1_183_714
+YYYYYYYYYYWYYYYWYWWUWWWQQ

metadata

@@ -1,109 +1,126 @@
 --- !ruby/object:Gem::Specification
 name: scbi_fastq
 version: !ruby/object:Gem::Version
-  version: 0.0.18
+  version: 0.0.19
 platform: ruby
 authors:
-- Dario Guerrero
+- dariogf
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-12-16 00:00:00.000000000 Z
+date: 2014-12-03 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
-  name: rdoc
+  name: scbi_multi_gz_reader
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - ">="
       - !ruby/object:Gem::Version
-        version: '4.0'
-  type: :development
+        version: '0'
+  type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - ">="
       - !ruby/object:Gem::Version
-        version: '4.0'
+        version: '0'
 - !ruby/object:Gem::Dependency
-  name: newgem
+  name: bundler
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.5.3
+        version: '1.7'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.5.3
+        version: '1.7'
 - !ruby/object:Gem::Dependency
-  name: hoe
+  name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.7'
+        version: '10.0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.7'
+        version: '10.0'
 description: scbi_fastq is a ruby gem to read/write FASTQ files (DNA/RNA sequences)
   with qualities in a variety of formats (Sanger, Solexa, Ilumina).
 email:
 - dariogf@scbi.uma.es
 executables: []
 extensions: []
-extra_rdoc_files:
-- History.txt
-- Manifest.txt
-- PostInstall.txt
-- README.rdoc
+extra_rdoc_files: []
 files:
-- History.txt
-- Manifest.txt
-- PostInstall.txt
-- README.rdoc
+- ".gitignore"
+- Gemfile
+- LICENSE.txt
+- README.md
 - Rakefile
 - lib/scbi_fastq.rb
 - lib/scbi_fastq/fastq_file.rb
-- script/console
-- script/destroy
-- script/generate
+- lib/scbi_fastq/version.rb
+- scbi_fastq.gemspec
+- test/final.fastq.gz
+- test/fq_all2std.pl
+- test/gz.rb
+- test/h1.fastq.gz
+- test/h2.fastq.gz
+- test/minitest.fastq.gz
+- test/prueba.rb
+- test/sanger.fastq
+- test/sanger.fastq.gz
+- test/sanger2.fastq
+- test/sanger2.fastq.gz
+- test/sanger_all.fastq.gz
+- test/scbi_fastq_test.rb
+- test/solexa.fastq
 - test/test_helper.rb
-- test/test_scbi_fastq.rb
-- .gemtest
-homepage: http://www.scbi.uma.es/downloads
+homepage: ''
 licenses:
 - MIT
 metadata: {}
-post_install_message: PostInstall.txt
-rdoc_options:
-- --main
-- README.rdoc
+post_install_message: 
+rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: scbi_fastq
-rubygems_version: 2.1.11
+rubyforge_project: 
+rubygems_version: 2.4.4
 signing_key: 
 specification_version: 4
-summary: scbi_fastq is a ruby gem to read/write FASTQ files (DNA/RNA sequences) with
-  qualities in a variety of formats (Sanger, Solexa, Ilumina).
+summary: read/write FASTQ files
 test_files:
-- test/test_scbi_fastq.rb
+- test/final.fastq.gz
+- test/fq_all2std.pl
+- test/gz.rb
+- test/h1.fastq.gz
+- test/h2.fastq.gz
+- test/minitest.fastq.gz
+- test/prueba.rb
+- test/sanger.fastq
+- test/sanger.fastq.gz
+- test/sanger2.fastq
+- test/sanger2.fastq.gz
+- test/sanger_all.fastq.gz
+- test/scbi_fastq_test.rb
+- test/solexa.fastq
 - test/test_helper.rb

data/History.txt

@@ -1,23 +0,0 @@
-=== 0.0.18 2013-12-16
-
-Write GZ
-
-=== 0.0.17 2012-07-13
-
-Read gzip files
-
-=== 0.0.16 2012-06-13
-
-Class method to_fastq saves with phred qualities
-
-=== 0.0.15 2012-05-24
-
-Uses default qual when no qual is present
-
-=== 0.0.14 2011-05-31
-
-release to rubygems
-
-=== 0.0.1 2010-11-29
-
-* Initial release

data/Manifest.txt

@@ -1,12 +0,0 @@
-History.txt
-Manifest.txt
-PostInstall.txt
-README.rdoc
-Rakefile
-lib/scbi_fastq.rb
-lib/scbi_fastq/fastq_file.rb
-script/console
-script/destroy
-script/generate
-test/test_helper.rb
-test/test_scbi_fastq.rb

data/PostInstall.txt

@@ -1,7 +0,0 @@
-
-For more information on scbi_fastq, see http://scbi_fastq.rubyforge.org
-
-NOTE: Change this information in PostInstall.txt 
-You can also delete it if you don't want it.
-
-

data/script/console

@@ -1,10 +0,0 @@
-#!/usr/bin/env ruby
-# File: script/console
-irb = RUBY_PLATFORM =~ /(:?mswin|mingw)/ ? 'irb.bat' : 'irb'
-
-libs =  " -r irb/completion"
-# Perhaps use a console_lib to store any extra methods I may want available in the cosole
-# libs << " -r #{File.dirname(__FILE__) + '/../lib/console_lib/console_logger.rb'}"
-libs <<  " -r #{File.expand_path(File.dirname(__FILE__) + '/../lib/scbi_fastq.rb')}"
-puts "Loading scbi_fastq gem"
-exec "#{irb} #{libs} --simple-prompt"

data/script/destroy

@@ -1,14 +0,0 @@
-#!/usr/bin/env ruby
-APP_ROOT = File.expand_path(File.join(File.dirname(__FILE__), '..'))
-
-begin
-  require 'rubigen'
-rescue LoadError
-  require 'rubygems'
-  require 'rubigen'
-end
-require 'rubigen/scripts/destroy'
-
-ARGV.shift if ['--help', '-h'].include?(ARGV[0])
-RubiGen::Base.use_component_sources! [:rubygems, :newgem, :newgem_theme, :test_unit]
-RubiGen::Scripts::Destroy.new.run(ARGV)

data/script/generate

@@ -1,14 +0,0 @@
-#!/usr/bin/env ruby
-APP_ROOT = File.expand_path(File.join(File.dirname(__FILE__), '..'))
-
-begin
-  require 'rubigen'
-rescue LoadError
-  require 'rubygems'
-  require 'rubigen'
-end
-require 'rubigen/scripts/generate'
-
-ARGV.shift if ['--help', '-h'].include?(ARGV[0])
-RubiGen::Base.use_component_sources! [:rubygems, :newgem, :newgem_theme, :test_unit]
-RubiGen::Scripts::Generate.new.run(ARGV)

data/test/test_scbi_fastq.rb

@@ -1,223 +0,0 @@
-require File.dirname(__FILE__) + '/test_helper.rb'
-
-class TestScbiFastq < Test::Unit::TestCase
-
-  def setup
-   	@test_file='/tmp/sanger.fastq';
-    @test_file_gz='/tmp/sanger.fastq.gz';
-   	
-  	
-  	@seq_fasta='ACTG'
-		@seq_qual=[31]
-	  @seq_name='SEQ'
-	  
-  end
-
-  def test_gz_sanger
-    
-		fqr=FastqFile.new(File.join(File.dirname(__FILE__),'sanger2.fastq.gz'))
-
-		i=1
-		
-		fqr.each do |n,s,q|
-
-		  assert_equal(@seq_name+i.to_s,n)
-		  assert_equal(@seq_fasta*i,s)
-		  assert_equal((@seq_qual*i*@seq_fasta.length),q)
-
-			i+=1
-		end
-		 
-	  fqr.close			
-
-    
-  end
-  
-  
-  def fill_file(n,offset=33)
-  	f=FastqFile.new(@test_file,'w')
-  	
-  	n.times do |c|
-  	  i = c+1
-  	  
-  	  name = "#{@seq_name+i.to_s}"
-  	  f.write_seq(name,@seq_fasta*i,(@seq_qual*i*@seq_fasta.length),'comments')
-      # f.puts('@'+name)
-      # f.puts(@seq_fasta*i)
-      # f.puts('+'+name)
-      # f.puts((@seq_qual*i*@seq_fasta.length).map{|e| (e+offset).chr}.join)
-  	end
-  	
-  	f.close
-  end
-
-  def fill_file_no_qual(n,offset=33)
-  	f=FastqFile.new(@test_file,'w')
-  	
-  	n.times do |c|
-  	  i = c+1
-  	  
-  	  name = "#{@seq_name+i.to_s}"
-  	  f.write_seq(name,@seq_fasta*i,'','comments')
-      # f.puts('@'+name)
-      # f.puts(@seq_fasta*i)
-      # f.puts('+'+name)
-      # f.puts((@seq_qual*i*@seq_fasta.length).map{|e| (e+offset).chr}.join)
-  	end
-  	
-  	f.close
-  end
-
-
-  def test_each
-
-    	 # make new file and fill with data
-		  fill_file(100) 	
-		
-
-			fqr=FastqFile.new(@test_file)
-
-			i=1
-			
-			fqr.each do |n,s,q|
-
-			  assert_equal(@seq_name+i.to_s,n)
-			  assert_equal(@seq_fasta*i,s)
-			  assert_equal((@seq_qual*i*@seq_fasta.length),q)
-
-				i+=1
-			end
-			 
-		  fqr.close			
-  end
-
-  def test_each_comments
-
-    	 # make new file and fill with data
-		  fill_file(100) 	
-		
-
-			fqr=FastqFile.new(@test_file)
-
-			i=1
-			
-			fqr.each do |n,s,q,c|
-			  
-			  assert_equal(@seq_name+i.to_s,n)
-			  assert_equal(@seq_fasta*i,s)
-			  assert_equal((@seq_qual*i*@seq_fasta.length),q)
-			  assert_equal('comments',c)
-
-				i+=1
-			end
-			 
-		  fqr.close			
-  end
-
-  def test_next_seq_comments
-
-    	 # make new file and fill with data
-		  fill_file(100)
-		
-
-			fqr=FastqFile.new(@test_file)
-
-			i=1
-			
-			begin
-			  n,s,q,c = fqr.next_seq
-
-			  if !n.nil?
-			  assert_equal(@seq_name+i.to_s,n)
-			  assert_equal(@seq_fasta*i,s)
-			  assert_equal((@seq_qual*i*@seq_fasta.length),q)
-			  assert_equal('comments',c)
-
-				i+=1
-			  end
-			end until n.nil?
-			 
-		  fqr.close
-  end
-  
-  def test_to_fastq
-    puts FastqFile.to_fastq(@seq_name,@seq_fasta*10,'','')
-    
-  end
-  
-  def test_each_no_qual
-
-    	 # make new file and fill with data
-		  fill_file_no_qual(100)
-		
-
-			fqr=FastqFile.new(@test_file,'r',:sanger, false,false)
-
-			i=1
-			
-			fqr.each do |n,s,q|
-        # puts n,s,q
-        assert_equal(@seq_name+i.to_s,n)
-        assert_equal(@seq_fasta*i,s)
-        # assert_equal((@seq_qual*i*@seq_fasta.length),q)
-
-				i+=1
-			end
-			 
-		  fqr.close			
-  end
-  
-
-  def fill_file_gz(n,offset=33)
-    f=FastqFile.new(@test_file_gz,'w.gz')
-    puts "FILE GZ"
-    n.times do |c|
-      i = c+1
-      
-      name = "#{@seq_name+i.to_s}"
-      f.write_seq(name,@seq_fasta*i,(@seq_qual*i*@seq_fasta.length),'comments')
-      # f.puts('@'+name)
-      # f.puts(@seq_fasta*i)
-      # f.puts('+'+name)
-      # f.puts((@seq_qual*i*@seq_fasta.length).map{|e| (e+offset).chr}.join)
-    end
-    
-    f.close
-  end
-
-  def test_each_gz
-           # make new file and fill with data
-      fill_file_gz(100)  
-    
-
-      fqr=FastqFile.new(@test_file_gz)
-
-      i=1
-      
-      fqr.each do |n,s,q|
-
-        assert_equal(@seq_name+i.to_s,n)
-        assert_equal(@seq_fasta*i,s)
-        assert_equal((@seq_qual*i*@seq_fasta.length),q)
-
-        i+=1
-      end
-      assert_equal(i,101)
-
-      fqr.close 
-  end
-
-  
-  # def test_open_file
-  #   fill_file(100)
-  #   fq=FastqFile.new('test/sanger.fastq')
-  #   
-  #   fq.each do |n,f,q|
-  #      puts n,f,q
-  #      puts fq.num_seqs
-  #   end
-  #   
-  #   fq.close
-  #   
-  # end
-end