bio-faster 0.2.0

data/.document

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+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/Gemfile

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+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "shoulda", ">= 0"
+  gem "bundler", "~> 1.0.0"
+  gem "jeweler", "~> 1.6.4"
+  gem "rcov", ">= 0"
+  gem "bio", ">= 1.4.2"
+  gem "rspec"
+end

data/Gemfile.lock

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+GEM
+  remote: http://rubygems.org/
+  specs:
+    bio (1.4.2)
+    diff-lcs (1.1.3)
+    git (1.2.5)
+    jeweler (1.6.4)
+      bundler (~> 1.0)
+      git (>= 1.2.5)
+      rake
+    rake (0.9.2.2)
+    rcov (0.9.11)
+    rcov (0.9.11-java)
+    rspec (2.7.0)
+      rspec-core (~> 2.7.0)
+      rspec-expectations (~> 2.7.0)
+      rspec-mocks (~> 2.7.0)
+    rspec-core (2.7.1)
+    rspec-expectations (2.7.0)
+      diff-lcs (~> 1.1.2)
+    rspec-mocks (2.7.0)
+    shoulda (2.11.3)
+
+PLATFORMS
+  java
+  ruby
+
+DEPENDENCIES
+  bio (>= 1.4.2)
+  bundler (~> 1.0.0)
+  jeweler (~> 1.6.4)
+  rcov
+  rspec
+  shoulda

data/LICENSE.txt

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+Copyright (c) 2011 Francesco Strozzi
+
+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.rdoc

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+= 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
+
+See the wiki page.
+
+
+== 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
+* Fork the project
+* Start a feature/bugfix branch
+* Commit and push until you are happy with your contribution
+* 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 (c) 2011 Francesco Strozzi. See LICENSE.txt for
+further details.
+

data/Rakefile

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+# encoding: utf-8
+
+require 'rubygems'
+require 'bundler'
+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 is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "bio-faster"
+  gem.homepage = "http://github.com/fstrozzi/bioruby-faster"
+  gem.license = "MIT"
+  gem.summary = %Q{A fast parser for Fasta and FastQ files}
+  gem.description = %Q{A fast parser for Fasta and FastQ files}
+  gem.email = "francesco.strozzi@gmail.com"
+  gem.authors = ["Francesco Strozzi"]
+  gem.required_ruby_version = '>= 1.9'
+  # dependencies defined in Gemfile
+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
+
+require 'rcov/rcovtask'
+Rcov::RcovTask.new do |test|
+  test.libs << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+  test.rcov_opts << '--exclude "gems/*"'
+end
+
+desc "Run all specs"
+task :spec do
+  FileList['spec/**/*_spec.rb'].each do |spec|
+    sh "rspec #{spec}"
+  end
+end
+
+task :default => :test
+
+require 'rake/rdoctask'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-faster #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end
+
+namespace :ext do
+  desc "Compile extension"
+  task :build do
+    puts "Building extension"
+    cd File.join(File.dirname(__FILE__),"ext")
+    sh "ruby "+File.join(File.dirname(__FILE__),"ext","extconf.rb")
+    sh "make"
+    FileList["*.log"].each do |file|
+      rm file
+    end
+    FileList["*.o"].each do |file|
+      rm file
+    end
+      
+  end
+end
+

data/VERSION

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+0.2.0

data/bio-faster.gemspec

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+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = "bio-faster"
+  s.version = "0.2.0"
+
+  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.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"
+  ]
+  s.files = [
+    ".document",
+    "Gemfile",
+    "Gemfile.lock",
+    "LICENSE.txt",
+    "README.rdoc",
+    "Rakefile",
+    "VERSION",
+    "bio-faster.gemspec",
+    "ext/extconf.rb",
+    "ext/faster.c",
+    "ext/kseq.h",
+    "lib/bio-faster.rb",
+    "spec/helper.rb",
+    "spec/parser_spec.rb",
+    "test/data/sample.fasta",
+    "test/data/sample.fastq",
+    "test/data/sample.fastq.gz",
+    "test/data/sff_sample.fastq"
+  ]
+  s.homepage = "http://github.com/fstrozzi/bioruby-faster"
+  s.licenses = ["MIT"]
+  s.require_paths = ["lib"]
+  s.required_ruby_version = Gem::Requirement.new(">= 1.9")
+  s.rubygems_version = "1.8.12"
+  s.summary = "A fast parser for Fasta and FastQ files"
+
+  if s.respond_to? :specification_version then
+    s.specification_version = 3
+
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_development_dependency(%q<shoulda>, [">= 0"])
+      s.add_development_dependency(%q<bundler>, ["~> 1.0.0"])
+      s.add_development_dependency(%q<jeweler>, ["~> 1.6.4"])
+      s.add_development_dependency(%q<rcov>, [">= 0"])
+      s.add_development_dependency(%q<bio>, [">= 1.4.2"])
+      s.add_development_dependency(%q<rspec>, [">= 0"])
+    else
+      s.add_dependency(%q<shoulda>, [">= 0"])
+      s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+      s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
+      s.add_dependency(%q<rcov>, [">= 0"])
+      s.add_dependency(%q<bio>, [">= 1.4.2"])
+      s.add_dependency(%q<rspec>, [">= 0"])
+    end
+  else
+    s.add_dependency(%q<shoulda>, [">= 0"])
+    s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+    s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
+    s.add_dependency(%q<rcov>, [">= 0"])
+    s.add_dependency(%q<bio>, [">= 1.4.2"])
+    s.add_dependency(%q<rspec>, [">= 0"])
+  end
+end
+

data/ext/extconf.rb

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+require 'mkmf'
+extension_name = "faster"
+have_library("z")
+create_makefile(extension_name)
+
+
+

data/ext/faster.c

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+/*
+Copyright(C) 2011 Francesco Strozzi <francesco.strozzi@gmail.com>
+*/
+
+#include <zlib.h>
+#include <stdio.h>
+#include "ruby.h"
+#include "kseq.h"
+
+KSEQ_INIT(gzFile, gzread)
+
+static VALUE method_parse(VALUE self, VALUE file) {
+
+	// check if a block is passed to the method
+	if (!(rb_block_given_p())) {
+		rb_raise(rb_eArgError,"You must pass a valid block!");
+	}
+
+	gzFile fp;
+	if (!(fp = gzopen(RSTRING_PTR(file), "r"))) {
+		rb_raise(rb_eArgError,"File %s not found!", RSTRING_PTR(file));
+	}
+	else {
+		kseq_t *seq;
+		seq = kseq_init(fp);
+		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));
+			rb_ary_push(arr, rb_str_new2(seq->seq.s));
+			if (seq->qual.l) {
+				VALUE rb_quality = rb_ary_new();
+				int unsigned i = 0;
+				while(i < seq->qual.l) {
+					rb_ary_push(rb_quality,INT2FIX(*(seq->qual.s + i) - 33)); // quality conversion (Sanger/Phred only)
+					i++;
+				}
+				rb_ary_push(arr,rb_quality);
+			}
+			rb_yield(arr);
+		}
+		kseq_destroy(seq);
+		gzclose(fp);
+		return Qtrue;
+	}
+}
+ 
+void Init_faster() {
+	VALUE Bio = rb_define_module("Bio");
+	VALUE Faster = rb_define_module_under(Bio,"Faster"); // it is defined as a sub-module of Bio
+	rb_define_singleton_method(Faster,"parse",method_parse,1);
+}

data/ext/kseq.h

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+/* The MIT License
+
+   Copyright (c) 2008 Genome Research Ltd (GRL).
+
+   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.
+*/
+
+/* Contact: Heng Li <lh3@sanger.ac.uk> */
+
+/* Last Modified: 12APR2009 */
+
+#ifndef AC_KSEQ_H
+#define AC_KSEQ_H
+
+#include <ctype.h>
+#include <string.h>
+#include <stdlib.h>
+
+#define KS_SEP_SPACE 0 // isspace(): \t, \n, \v, \f, \r
+#define KS_SEP_TAB   1 // isspace() && !' '
+#define KS_SEP_MAX   1
+
+#define __KS_TYPE(type_t)						\
+	typedef struct __kstream_t {				\
+		char *buf;								\
+		int begin, end, is_eof;					\
+		type_t f;								\
+	} kstream_t;
+
+#define ks_eof(ks) ((ks)->is_eof && (ks)->begin >= (ks)->end)
+#define ks_rewind(ks) ((ks)->is_eof = (ks)->begin = (ks)->end = 0)
+
+#define __KS_BASIC(type_t, __bufsize)								\
+	static inline kstream_t *ks_init(type_t f)						\
+	{																\
+		kstream_t *ks = (kstream_t*)calloc(1, sizeof(kstream_t));	\
+		ks->f = f;													\
+		ks->buf = (char*)malloc(__bufsize);							\
+		return ks;													\
+	}																\
+	static inline void ks_destroy(kstream_t *ks)					\
+	{																\
+		if (ks) {													\
+			free(ks->buf);											\
+			free(ks);												\
+		}															\
+	}
+
+#define __KS_GETC(__read, __bufsize)						\
+	static inline int ks_getc(kstream_t *ks)				\
+	{														\
+		if (ks->is_eof && ks->begin >= ks->end) return -1;	\
+		if (ks->begin >= ks->end) {							\
+			ks->begin = 0;									\
+			ks->end = __read(ks->f, ks->buf, __bufsize);	\
+			if (ks->end < __bufsize) ks->is_eof = 1;		\
+			if (ks->end == 0) return -1;					\
+		}													\
+		return (int)ks->buf[ks->begin++];					\
+	}
+
+#ifndef KSTRING_T
+#define KSTRING_T kstring_t
+typedef struct __kstring_t {
+	size_t l, m;
+	char *s;
+} kstring_t;
+#endif
+
+#ifndef kroundup32
+#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
+#endif
+
+#define __KS_GETUNTIL(__read, __bufsize)								\
+	static int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \
+	{																	\
+		if (dret) *dret = 0;											\
+		str->l = 0;														\
+		if (ks->begin >= ks->end && ks->is_eof) return -1;				\
+		for (;;) {														\
+			int i;														\
+			if (ks->begin >= ks->end) {									\
+				if (!ks->is_eof) {										\
+					ks->begin = 0;										\
+					ks->end = __read(ks->f, ks->buf, __bufsize);		\
+					if (ks->end < __bufsize) ks->is_eof = 1;			\
+					if (ks->end == 0) break;							\
+				} else break;											\
+			}															\
+			if (delimiter > KS_SEP_MAX) {								\
+				for (i = ks->begin; i < ks->end; ++i)					\
+					if (ks->buf[i] == delimiter) break;					\
+			} else if (delimiter == KS_SEP_SPACE) {						\
+				for (i = ks->begin; i < ks->end; ++i)					\
+					if (isspace(ks->buf[i])) break;						\
+			} else if (delimiter == KS_SEP_TAB) {						\
+				for (i = ks->begin; i < ks->end; ++i)					\
+					if (isspace(ks->buf[i]) && ks->buf[i] != ' ') break; \
+			} else i = 0; /* never come to here! */						\
+			if (str->m - str->l < i - ks->begin + 1) {					\
+				str->m = str->l + (i - ks->begin) + 1;					\
+				kroundup32(str->m);										\
+				str->s = (char*)realloc(str->s, str->m);				\
+			}															\
+			memcpy(str->s + str->l, ks->buf + ks->begin, i - ks->begin); \
+			str->l = str->l + (i - ks->begin);							\
+			ks->begin = i + 1;											\
+			if (i < ks->end) {											\
+				if (dret) *dret = ks->buf[i];							\
+				break;													\
+			}															\
+		}																\
+		if (str->l == 0) {												\
+			str->m = 1;													\
+			str->s = (char*)calloc(1, 1);								\
+		}																\
+		str->s[str->l] = '\0';											\
+		return str->l;													\
+	}
+
+#define KSTREAM_INIT(type_t, __read, __bufsize) \
+	__KS_TYPE(type_t)							\
+	__KS_BASIC(type_t, __bufsize)				\
+	__KS_GETC(__read, __bufsize)				\
+	__KS_GETUNTIL(__read, __bufsize)
+
+#define __KSEQ_BASIC(type_t)											\
+	static inline kseq_t *kseq_init(type_t fd)							\
+	{																	\
+		kseq_t *s = (kseq_t*)calloc(1, sizeof(kseq_t));					\
+		s->f = ks_init(fd);												\
+		return s;														\
+	}																	\
+	static inline void kseq_rewind(kseq_t *ks)							\
+	{																	\
+		ks->last_char = 0;												\
+		ks->f->is_eof = ks->f->begin = ks->f->end = 0;					\
+	}																	\
+	static inline void kseq_destroy(kseq_t *ks)							\
+	{																	\
+		if (!ks) return;												\
+		free(ks->name.s); free(ks->comment.s); free(ks->seq.s);	free(ks->qual.s); \
+		ks_destroy(ks->f);												\
+		free(ks);														\
+	}
+
+/* Return value:
+   >=0  length of the sequence (normal)
+   -1   end-of-file
+   -2   truncated quality string
+ */
+#define __KSEQ_READ														\
+	static int kseq_read(kseq_t *seq)									\
+	{																	\
+		int c;															\
+		kstream_t *ks = seq->f;											\
+		if (seq->last_char == 0) { /* then jump to the next header line */ \
+			while ((c = ks_getc(ks)) != -1 && c != '>' && c != '@');	\
+			if (c == -1) return -1; /* end of file */					\
+			seq->last_char = c;											\
+		} /* the first header char has been read */						\
+		seq->comment.l = seq->seq.l = seq->qual.l = 0;					\
+		if (ks_getuntil(ks, 0, &seq->name, &c) < 0) return -1;			\
+		if (c != '\n') ks_getuntil(ks, '\n', &seq->comment, 0);			\
+		while ((c = ks_getc(ks)) != -1 && c != '>' && c != '+' && c != '@') { \
+			if (isgraph(c)) { /* printable non-space character */		\
+				if (seq->seq.l + 1 >= seq->seq.m) { /* double the memory */ \
+					seq->seq.m = seq->seq.l + 2;						\
+					kroundup32(seq->seq.m); /* rounded to next closest 2^k */ \
+					seq->seq.s = (char*)realloc(seq->seq.s, seq->seq.m); \
+				}														\
+				seq->seq.s[seq->seq.l++] = (char)c;						\
+			}															\
+		}																\
+		if (c == '>' || c == '@') seq->last_char = c; /* the first header char has been read */	\
+		seq->seq.s[seq->seq.l] = 0;	/* null terminated string */		\
+		if (c != '+') return seq->seq.l; /* FASTA */					\
+		if (seq->qual.m < seq->seq.m) {	/* allocate enough memory */	\
+			seq->qual.m = seq->seq.m;									\
+			seq->qual.s = (char*)realloc(seq->qual.s, seq->qual.m);		\
+		}																\
+		while ((c = ks_getc(ks)) != -1 && c != '\n'); /* skip the rest of '+' line */ \
+		if (c == -1) return -2; /* we should not stop here */			\
+		while ((c = ks_getc(ks)) != -1 && seq->qual.l < seq->seq.l)		\
+			if (c >= 33 && c <= 127) seq->qual.s[seq->qual.l++] = (unsigned char)c;	\
+		seq->qual.s[seq->qual.l] = 0; /* null terminated string */		\
+		seq->last_char = 0;	/* we have not come to the next header line */ \
+		if (seq->seq.l != seq->qual.l) return -2; /* qual string is shorter than seq string */ \
+		return seq->seq.l;												\
+	}
+
+#define __KSEQ_TYPE(type_t)						\
+	typedef struct {							\
+		kstring_t name, comment, seq, qual;		\
+		int last_char;							\
+		kstream_t *f;							\
+	} kseq_t;
+
+#define KSEQ_INIT(type_t, __read)				\
+	KSTREAM_INIT(type_t, __read, 4096)			\
+	__KSEQ_TYPE(type_t)							\
+	__KSEQ_BASIC(type_t)						\
+	__KSEQ_READ
+
+#endif

data/lib/bio-faster.rb

@@ -0,0 +1,6 @@
+#
+# Copyright(C) 2011 Francesco Strozzi <francesco.strozzi@gmail.com>
+#
+
+require File.expand_path(File.join(File.dirname(__FILE__),'..','ext','faster'))
+

data/spec/helper.rb

@@ -0,0 +1,18 @@
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+
+require 'rspec'
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+TEST_DATA = File.join(File.dirname(File.dirname(__FILE__)),"test","data")
+require 'bio-faster'
+require 'bio'
+

data/spec/parser_spec.rb

@@ -0,0 +1,117 @@
+require 'helper'
+
+describe Bio::Faster do
+  
+  describe "#parser" do
+  
+    it "reads both Fasta and FastQ format files" do
+      res = Bio::Faster.parse(File.join(TEST_DATA,"sample.fastq")) {|seq|}
+      res.should == true
+      res = Bio::Faster.parse(File.join(TEST_DATA,"sample.fasta")) {|seq|}
+      res.should == true
+    end
+    
+    it "needs a valid block to parse files" do
+      expect { Bio::Faster.parse(File.join(TEST_DATA,"sample.fastq")) }.to raise_error(ArgumentError)
+    end
+  
+    it "throws an error if file does not exists" do
+      expect { Bio::Faster.parse(File.join(TEST_DATA,"dummy.fastq")) }.to raise_error(ArgumentError)
+    end
+    
+    it "returns an array with id, comment, sequence and an array with qualities (FastQ only)" do
+      Bio::Faster.parse(File.join(TEST_DATA,"sample.fastq")) do |seq| 
+        seq.class.should == Array
+        seq.size.should == 4
+        seq[-1].class.should == Array
+      end
+      
+      Bio::Faster.parse(File.join(TEST_DATA,"sample.fasta")) do |seq| 
+        seq.class.should == Array
+        seq.size.should == 3
+      end
+      
+    end
+    
+    it "reads gzipped files" do
+      res = Bio::Faster.parse(File.join(TEST_DATA,"sample.fastq")) {|seq|}
+      res.should == true
+    end
+    
+    it "parse correctly FastQ files" do
+      faster_res = []
+      Bio::Faster.parse(File.join(TEST_DATA,"sample.fastq")) {|seq| faster_res << seq}
+      faster_res[0][0].should == "HISEQ1:86:D0306ACXX:2:1101:20970:17588"
+      faster_res[0][1].should == "1:N:0:CTTGTA"
+      faster_res[0][2].should == "CGGTGCTGTTGTTATGCTGATGCTTATTAGTGCAAGTGTAGCTCCTCCGATTAGATGAATTAACAGGTGTCCTGCAGTAATGTTGGCTGTTAGTCGTAC"
+      
+      faster_res[-1][0].should == "HISEQ1:86:D0306ACXX:2:1101:1411:17830"
+      faster_res[-1][1].should == "1:Y:0:CTTGTA"
+      faster_res[-1][2].should == "CGGCGGGCGTGGGGAGAGAGCTATGAAGGCCTCAGGGAAGCTTCGAGAGTATAAGGTGTTGGGGTGCTGCCTGCCAACCCCCAAATTCCACACACCACC"
+    end
+    
+    it "parse correctly compressed FastQ files" do
+      faster_res = []
+      Bio::Faster.parse(File.join(TEST_DATA,"sample.fastq.gz")) {|seq| faster_res << seq}
+      faster_res[0][0].should == "HISEQ1:86:D0306ACXX:2:1101:20970:17588"
+      faster_res[0][1].should == "1:N:0:CTTGTA"
+      faster_res[0][2].should == "CGGTGCTGTTGTTATGCTGATGCTTATTAGTGCAAGTGTAGCTCCTCCGATTAGATGAATTAACAGGTGTCCTGCAGTAATGTTGGCTGTTAGTCGTAC"
+      
+      faster_res[-1][0].should == "HISEQ1:86:D0306ACXX:2:1101:1411:17830"
+      faster_res[-1][1].should == "1:Y:0:CTTGTA"
+      faster_res[-1][2].should == "CGGCGGGCGTGGGGAGAGAGCTATGAAGGCCTCAGGGAAGCTTCGAGAGTATAAGGTGTTGGGGTGCTGCCTGCCAACCCCCAAATTCCACACACCACC"
+    end
+    
+
+    it "parse correctly Fasta files" do
+      faster_res = []
+      Bio::Faster.parse(File.join(TEST_DATA,"sample.fasta")) {|seq| faster_res << seq}
+      faster_res[0][0].should == "seq1"
+      faster_res[0][1].should == "comment1"
+      faster_res[0][2].should == "AGCAATTTCCCTTTTCCTGTCCTTTTTATAACATTGTGGAGGAAGACGGCAGCATAAAAAGGACAGTATTTGATTAAAAAATGATAAAAATTTTCAAAC"
+      
+      faster_res[-1][0].should == "seq4"
+      faster_res[-1][1].should == "comment4"
+      faster_res[-1][2].should == "mgltrrealssiaavggekalkdalavlggps"
+    end
+  
+  
+    describe "quality conversion for FastQ files (Sanger/Phred only)" do
+    
+      it "converts directly quality scores for Illumina 1.8+ FastQ files" do
+
+        bioruby_quals = []
+        # standard Quality conversion as done in BioRuby Bio::FastQ
+        Bio::FlatFile.open(Bio::Fastq,File.open(File.join(TEST_DATA,"sample.fastq"))).each_entry do |seq|
+          bioruby_quals << seq.qualities
+        end
+
+        faster_quals = []
+        Bio::Faster.parse(File.join(TEST_DATA,"sample.fastq")) do |seq|
+          faster_quals << seq[-1]
+        end
+        faster_quals.should == bioruby_quals
+
+      end
+
+      it "converts directly quality scores for SFF 454 FastQ files" do
+
+        bioruby_quals = []
+        # standard Quality conversion as done in BioRuby Bio::FastQ
+        Bio::FlatFile.open(Bio::Fastq,File.open(File.join(TEST_DATA,"sff_sample.fastq"))).each_entry do |seq|
+          bioruby_quals << seq.qualities
+        end
+
+        faster_quals = []
+        Bio::Faster.parse(File.join(TEST_DATA,"sff_sample.fastq")) do |seq|
+          faster_quals << seq[-1]
+        end
+        faster_quals.should == bioruby_quals
+
+      end
+    
+    end
+  
+  end
+  
+end

data/test/data/sample.fasta

@@ -0,0 +1,10 @@
+>seq1 comment1
+AGCAATTTCCCTTTTCCTGTCCTTTTTATAACATTGTGGAGGAAGACGGCAGCATAAAAAGGACAGTATTTGATTAAAAAATGATAAAAATTTTCAAAC 
+>seq2 comment 2
+GTGGGGCCAAAGGGGTTTGGAGGTGCCTTGTTCTTAGTCCCCAGAAGACTAGAGAGACTGCGTTTCAGGGAGGAGGAGATAAGACGAGCAGGAGACTTC 
+
+>seq3 comment3
+CTCATAGACACGGTCCGAGGAGCCAAACACCAAGCTGTTGGGGAAGACTCGGCTGAGGAACTGCAGGGGCCCAAGCCACGACTGGATGAGGAGCAGTGA 
+
+>seq4 comment4
+mgltrrealssiaavggekalkdalavlggps 

data/test/data/sample.fastq

@@ -0,0 +1,24 @@
+@HISEQ1:86:D0306ACXX:2:1101:20970:17588 1:N:0:CTTGTA
+CGGTGCTGTTGTTATGCTGATGCTTATTAGTGCAAGTGTAGCTCCTCCGATTAGATGAATTAACAGGTGTCCTGCAGTAATGTTGGCTGTTAGTCGTAC
++
+@C@:DDFFHGHHHIJJJJIGIJIJJCHIGGHGIIJJGGHGIJIGJJIJJGGIIBGGCFIAFGF4CGI;AHIFGIEHEEH>EDFFEFFD@AECCDCBDD<
+@HISEQ1:86:D0306ACXX:2:1101:20839:17705 1:N:0:CTTGTA
+AGCAATTTCCCTTTTCCTGTCCTTTTTATAACATTGTGGAGGAAGACGGCAGCATAAAAAGGACAGTATTTGATTAAAAAATGATAAAAATTTTCAAAC
++
+@@<DFFFFHBDHHJEAFHIJJEHIIIJGHGIGEHGEEGGCGGDG>@GB:@DBGGIIGBGEHHIGFE:@A?B>?>;>>>@;>BCA@>ACCC?:A>;>>@3
+@HISEQ1:86:D0306ACXX:2:1101:21047:17715 1:Y:0:CTTGTA
+GTTAAGAATCTGCCTGCCAATGCAGGAGATGCAAGAGATGCAAGAGACGTGGGTTCCATAGCTGGGTCAGGAAAATTACCTGAAGGAGGACATATCAAA
++
+=7+2?@++?4?7A7+++<+++3+3<AA<;3A@A9AA###############################################################
+@HISEQ1:86:D0306ACXX:2:1101:21299:17513 1:N:0:CTTGTA
+GTAGCACACTTTCACTATGTCCTATCAATAGGAGCTGTGTTCGCCATTATAGGAGGATTTGTAAATTGATTTCCACTGTTCTCATACTATAACCTAAAA
++
+8:?;=;B?;B>+A,<AEACEDE@AFF,A:99CEF@E*1??:CDII:?@*9?@*9D:BCB@.88>AAAA)==4==7=C;==);@################
+@HISEQ1:86:D0306ACXX:2:1101:1352:17782 1:N:0:CTTGTA
+AATAATTGTTTGCATTGCCTTTTATATATATTTATATATATATATAAAACATGGGTCTTGGTTTTTTGATTTATTAGTGTGAAGAAATAACTACATTCT
++
+@<?DABADHGFA<,CECFIHGIIDEGG@DHGDGI<<CHEBCEGIIIGCD<CFGC=09?<F@GEHIDHI=A:C;EH>3?EE;?C@@DDFA>@>@>C3;AC
+@HISEQ1:86:D0306ACXX:2:1101:1411:17830 1:Y:0:CTTGTA
+CGGCGGGCGTGGGGAGAGAGCTATGAAGGCCTCAGGGAAGCTTCGAGAGTATAAGGTGTTGGGGTGCTGCCTGCCAACCCCCAAATTCCACACACCACC
++
+###################################################################################################

data/test/data/sff_sample.fastq

@@ -0,0 +1,16 @@
+@SRR014849.1 EIXKN4201CFU84/1
+GGGGGGGGGGGGGGGGCTTTTTTTGTTTGGAACCGAAAGGGTTTTGAATTTCAAACCCTTTTCGGTTTCCAACCTTCCAAAGCAATGCCAATACTGAGCGGGCTGGCAAGGCNNNNNNNNNNNN
++
+3+&$#"""""""""""7F@71,'";C?,B;?6B;:EA1EA1EA5'9B:?:#9EA0D@2EA5':>5?:%A;A8A;?9B;D@/=<?7=9<2A8==<=5<6:?:$::9.;:0:/3!!!!!!!!!!!!
+@SRR014849.2 EIXKN4201AKDUH/1
+TCAAGTGGTGAACGGCAGAAA
++
+<=B:==B:=<?6=B;<;=B=)
+@SRR014849.3 EIXKN4201D4ZBL/1
+GGGGGGGGGCTGTTGGCCGAGGTTGGAGTAGCCAGGGGGAAGGCATGGCCAGCCGTTGAGAAATGCTTGTTGAAGTTTTCGATAATAATGGATTTATCGGTGGTGACCGTGTTACCTAGCC
++
+;3.*(&$"";<=A9@8A9;<B;B;B;8=<==B;<FB8/'@8B:==<B;A9<<A8=B;==;A=)=<<B;=A9<@7<FB5(<<=<B;<B;:A9=EA0;<;B:<A8=<<@8<<<B;<A99=<B:
+@SRR014849.4 EIXKN4201AHFLR/1
+GGGGTTCAAGAATATGCCCC
++
+B8/&?9<B;=B;=<9<FB5(

metadata

@@ -0,0 +1,132 @@
+--- !ruby/object:Gem::Specification
+name: bio-faster
+version: !ruby/object:Gem::Version
+  version: 0.2.0
+  prerelease: 
+platform: ruby
+authors:
+- Francesco Strozzi
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2012-01-04 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: shoulda
+  requirement: &2154318860 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: *2154318860
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: &2154318380 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.0.0
+  type: :development
+  prerelease: false
+  version_requirements: *2154318380
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: &2154317900 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.6.4
+  type: :development
+  prerelease: false
+  version_requirements: *2154317900
+- !ruby/object:Gem::Dependency
+  name: rcov
+  requirement: &2154317360 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: *2154317360
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: &2154316860 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+  type: :development
+  prerelease: false
+  version_requirements: *2154316860
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: &2154316360 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: *2154316360
+description: A fast parser for Fasta and FastQ files
+email: francesco.strozzi@gmail.com
+executables: []
+extensions:
+- ext/extconf.rb
+extra_rdoc_files:
+- LICENSE.txt
+- README.rdoc
+files:
+- .document
+- Gemfile
+- Gemfile.lock
+- LICENSE.txt
+- README.rdoc
+- Rakefile
+- VERSION
+- bio-faster.gemspec
+- ext/extconf.rb
+- ext/faster.c
+- ext/kseq.h
+- lib/bio-faster.rb
+- spec/helper.rb
+- spec/parser_spec.rb
+- test/data/sample.fasta
+- test/data/sample.fastq
+- test/data/sample.fastq.gz
+- test/data/sff_sample.fastq
+homepage: http://github.com/fstrozzi/bioruby-faster
+licenses:
+- MIT
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '1.9'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.12
+signing_key: 
+specification_version: 3
+summary: A fast parser for Fasta and FastQ files
+test_files: []