bio-faster 0.2.1 → 0.2.2

data/.travis.yml

@@ -0,0 +1,12 @@
+language: ruby
+rvm:
+  - 1.8.7
+  - 1.9.2
+  - 1.9.3
+ # - jruby-18mode # JRuby in 1.8 mode
+ # - jruby-19mode # JRuby in 1.9 mode
+ # - rbx-18mode
+ # - rbx-19mode
+# uncomment this line if your project needs to run something other than `rake`:
+#script: bundle exec rake ext:build
+#script: bundle exec rake

data/{README.rdoc → README.md}

@@ -1,14 +1,21 @@
-= bio-faster
+[![Build Status](https://secure.travis-ci.org/fstrozzi/bioruby-faster.png?branch=master)](http://travis-ci.org/fstrozzi/bioruby-faster)
+
+Bio::Faster
+==========
 
 Fast and simple parser for FastA / FastQ files, based on Heng Li Kseq library written in C.
 http://lh3lh3.users.sourceforge.net/parsefastq.shtml
 
-= Examples
+Examples
+========
+
+[See the wiki page](https://github.com/fstrozzi/bioruby-faster/wiki)
 
-See the wiki page.
+[See the specs](https://github.com/fstrozzi/bioruby-faster/blob/master/spec/parser_spec.rb)
 
 
-== Contributing to bio-faster
+Contributing to bio-faster
+==========================
  
 * Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet
 * Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it
@@ -18,7 +25,8 @@ See the wiki page.
 * Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
 * Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
 
-== Copyright
+Copyright
+=========
 
 Copyright (c) 2011 Francesco Strozzi. See LICENSE.txt for
 further details.

data/Rakefile

@@ -41,15 +41,12 @@ Rcov::RcovTask.new do |test|
   test.rcov_opts << '--exclude "gems/*"'
 end
 
-desc "Run all specs"
-task :spec do
-  FileList['spec/**/*_spec.rb'].each do |spec|
-    sh "rspec #{spec}"
-  end
+require 'rspec/core'
+require 'rspec/core/rake_task'
+RSpec::Core::RakeTask.new(:spec) do |spec|
+  spec.pattern = FileList['spec/**/*_spec.rb']
 end
 
-task :default => :test
-
 require 'rake/rdoctask'
 Rake::RDocTask.new do |rdoc|
   version = File.exist?('VERSION') ? File.read('VERSION') : ""
@@ -73,7 +70,9 @@ namespace :ext do
     FileList["*.o"].each do |file|
       rm file
     end
-      
+    cd ".."  
   end
 end
 
+task :default => ["ext:build",:spec]
+

data/VERSION

@@ -1 +1 @@
-0.2.1
+0.2.2

data/bio-faster.gemspec

@@ -5,24 +5,25 @@
 
 Gem::Specification.new do |s|
   s.name = "bio-faster"
-  s.version = "0.2.1"
+  s.version = "0.2.2"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Francesco Strozzi"]
-  s.date = "2012-01-04"
+  s.date = "2012-04-02"
   s.description = "A fast parser for Fasta and FastQ files"
   s.email = "francesco.strozzi@gmail.com"
   s.extensions = ["ext/extconf.rb"]
   s.extra_rdoc_files = [
     "LICENSE.txt",
-    "README.rdoc"
+    "README.md"
   ]
   s.files = [
     ".document",
+    ".travis.yml",
     "Gemfile",
     "Gemfile.lock",
     "LICENSE.txt",
-    "README.rdoc",
+    "README.md",
     "Rakefile",
     "VERSION",
     "bio-faster.gemspec",
@@ -41,7 +42,7 @@ Gem::Specification.new do |s|
   s.licenses = ["MIT"]
   s.require_paths = ["lib"]
   s.required_ruby_version = Gem::Requirement.new(">= 1.9")
-  s.rubygems_version = "1.8.12"
+  s.rubygems_version = "1.8.15"
   s.summary = "A fast parser for Fasta and FastQ files"
 
   if s.respond_to? :specification_version then

data/ext/faster.c

@@ -26,7 +26,12 @@ static VALUE method_parse(VALUE self, VALUE file) {
 		while (kseq_read(seq) >= 0) {
 			VALUE arr = rb_ary_new();
 			rb_ary_push(arr, rb_str_new2(seq->name.s));
-			if (seq->comment.l) rb_ary_push(arr, rb_str_new2(seq->comment.s));
+			if (seq->comment.l) {
+				rb_ary_push(arr, rb_str_new2(seq->comment.s));
+			}
+			else {
+				rb_ary_push(arr, Qnil);
+			}	
 			rb_ary_push(arr, rb_str_new2(seq->seq.s));
 			if (seq->qual.l) {
 				VALUE rb_quality = rb_ary_new();

data/spec/parser_spec.rb

@@ -71,10 +71,30 @@ describe Bio::Faster do
       faster_res[0][2].should == "AGCAATTTCCCTTTTCCTGTCCTTTTTATAACATTGTGGAGGAAGACGGCAGCATAAAAAGGACAGTATTTGATTAAAAAATGATAAAAATTTTCAAAC"
       
       faster_res[-1][0].should == "seq4"
-      faster_res[-1][1].should == "comment4"
+      faster_res[-1][1].should == nil
       faster_res[-1][2].should == "mgltrrealssiaavggekalkdalavlggps"
     end
   
+    it "can return the sequence data in a more friendly way" do
+      Bio::Faster.parse(File.join(TEST_DATA,"sample.fastq")) do |sequence_id, comment, sequence, quality|
+        sequence_id.should == "HISEQ1:86:D0306ACXX:2:1101:20970:17588"
+        comment.should == "1:N:0:CTTGTA"
+        sequence.should == "CGGTGCTGTTGTTATGCTGATGCTTATTAGTGCAAGTGTAGCTCCTCCGATTAGATGAATTAACAGGTGTCCTGCAGTAATGTTGGCTGTTAGTCGTAC"
+        quality.class.should == Array 
+        break
+      end
+    end
+    
+    it "can return the sequence data in a more friendly way (also for FastA)" do
+      Bio::Faster.parse(File.join(TEST_DATA,"sample.fasta")) do |sequence_id, comment, sequence, quality|
+        quality.should == nil # it is a Fasta file, so no quality
+        sequence_id.should == "seq1"
+        comment.should == "comment1"
+        sequence.should == "AGCAATTTCCCTTTTCCTGTCCTTTTTATAACATTGTGGAGGAAGACGGCAGCATAAAAAGGACAGTATTTGATTAAAAAATGATAAAAATTTTCAAAC"
+        break
+      end
+    end
+  
   
     describe "quality conversion for FastQ files (Sanger/Phred only)" do
     
@@ -87,8 +107,8 @@ describe Bio::Faster do
         end
 
         faster_quals = []
-        Bio::Faster.parse(File.join(TEST_DATA,"sample.fastq")) do |seq|
-          faster_quals << seq[-1]
+        Bio::Faster.parse(File.join(TEST_DATA,"sample.fastq")) do |sequence_id, comment, sequence, quality|
+          faster_quals << quality
         end
         faster_quals.should == bioruby_quals
 
@@ -103,8 +123,8 @@ describe Bio::Faster do
         end
 
         faster_quals = []
-        Bio::Faster.parse(File.join(TEST_DATA,"sff_sample.fastq")) do |seq|
-          faster_quals << seq[-1]
+        Bio::Faster.parse(File.join(TEST_DATA,"sff_sample.fastq")) do |sequence_id, comment, sequence, quality|
+          faster_quals << quality
         end
         faster_quals.should == bioruby_quals
 

data/test/data/sample.fasta

@@ -6,5 +6,5 @@ GTGGGGCCAAAGGGGTTTGGAGGTGCCTTGTTCTTAGTCCCCAGAAGACTAGAGAGACTGCGTTTCAGGGAGGAGGAGAT
 >seq3 comment3
 CTCATAGACACGGTCCGAGGAGCCAAACACCAAGCTGTTGGGGAAGACTCGGCTGAGGAACTGCAGGGGCCCAAGCCACGACTGGATGAGGAGCAGTGA 
 
->seq4 comment4
+>seq4
 mgltrrealssiaavggekalkdalavlggps 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-faster
 version: !ruby/object:Gem::Version
-  version: 0.2.1
+  version: 0.2.2
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-01-04 00:00:00.000000000 Z
+date: 2012-04-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &2161466300 !ruby/object:Gem::Requirement
+  requirement: &2161251160 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2161466300
+  version_requirements: *2161251160
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &2161465800 !ruby/object:Gem::Requirement
+  requirement: &2161250660 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -32,10 +32,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *2161465800
+  version_requirements: *2161250660
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &2161465320 !ruby/object:Gem::Requirement
+  requirement: &2161250100 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -43,10 +43,10 @@ dependencies:
         version: 1.6.4
   type: :development
   prerelease: false
-  version_requirements: *2161465320
+  version_requirements: *2161250100
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &2161464780 !ruby/object:Gem::Requirement
+  requirement: &2161249560 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,10 +54,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2161464780
+  version_requirements: *2161249560
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &2161464280 !ruby/object:Gem::Requirement
+  requirement: &2161249020 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -65,10 +65,10 @@ dependencies:
         version: 1.4.2
   type: :development
   prerelease: false
-  version_requirements: *2161464280
+  version_requirements: *2161249020
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &2161463780 !ruby/object:Gem::Requirement
+  requirement: &2161248500 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -76,7 +76,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2161463780
+  version_requirements: *2161248500
 description: A fast parser for Fasta and FastQ files
 email: francesco.strozzi@gmail.com
 executables: []
@@ -84,13 +84,14 @@ extensions:
 - ext/extconf.rb
 extra_rdoc_files:
 - LICENSE.txt
-- README.rdoc
+- README.md
 files:
 - .document
+- .travis.yml
 - Gemfile
 - Gemfile.lock
 - LICENSE.txt
-- README.rdoc
+- README.md
 - Rakefile
 - VERSION
 - bio-faster.gemspec
@@ -125,7 +126,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.12
+rubygems_version: 1.8.15
 signing_key: 
 specification_version: 3
 summary: A fast parser for Fasta and FastQ files