Complete rename.

bio-kseq.gemspec

@@ -0,0 +1,28 @@
+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'bio/kseq/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "bio-kseq"
+  spec.version       = Bio::Kseq::VERSION
+  spec.authors       = ["Gusev Fedor"]
+  spec.email         = ["gusevfe@gmail.com"]
+  spec.summary       = %q{Ruby inferface for Heng Li kseq.h}
+  spec.description   = %q{A fast FASTA/FASTQ parser based on kseq.h by Heng Li}
+  spec.homepage      = ""
+  spec.license       = "MIT"
+
+  spec.files         = `git ls-files -z`.split("\x0")
+  spec.files         << "ext/seqtk_bindings/seqtk/kseq.h"
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ["lib", "ext"]
+  spec.extensions    = Dir['ext/**/extconf.rb']
+  spec.platform = Gem::Platform::RUBY
+
+  spec.add_development_dependency "bundler", "~> 1.5"
+  spec.add_development_dependency "rake"
+  spec.add_development_dependency "rspec"
+  spec.add_development_dependency "rake-compiler"
+end

ext/seqtk_bindings/seqtk_bindings.c

@@ -14,7 +14,6 @@ static void kseq_wrapper_deallocate(void *seq);
 static VALUE kseq_wrapper_read(VALUE self);
 
 VALUE mBio;
-VALUE mSeqtk;
 VALUE cKseq;
 
 typedef struct {
@@ -23,15 +22,6 @@ typedef struct {
   gzFile fp;
 } Kseq_Wrapper;
 
-FILE *rb_io_stdio_file(rb_io_t *fptr)
-{
-  if (!fptr->stdio_file) {
-    int oflags = rb_io_fmode_oflags(fptr->mode);
-    fptr->stdio_file = rb_fdopen(fptr->fd, rb_io_oflags_modestr(oflags));
-  }
-  return fptr->stdio_file;
-}
-
 #define kseq_wrapper_field(NAME) \
   static VALUE kseq_wrapper_ ## NAME(VALUE self) { \
     Kseq_Wrapper *w; \
@@ -49,8 +39,7 @@ kseq_wrapper_field(qual);
 
 void Init_seqtk_bindings() {
   mBio = rb_define_module("Bio");
-  mSeqtk = rb_define_module_under(mBio, "SeqTK");
-  cKseq = rb_define_class_under(mSeqtk, "Kseq", rb_cObject);
+  cKseq = rb_define_class_under(mBio, "Kseq", rb_cObject);
   rb_define_alloc_func(cKseq, kseq_wrapper_allocate);
   rb_define_method(cKseq, "initialize", kseq_wrapper_initialize, 1);
 

lib/bio/kseq.rb

@@ -0,0 +1,24 @@
+require "seqtk_bindings/seqtk_bindings"
+require "bio/kseq/version"
+
+module Bio
+  module SeqTK
+    class Kseq
+      def to_s
+        if qual.nil?
+          if comment.nil?
+            ">" + name + "\n" + seq
+          else
+            ">" + name + " " + comment + "\n" + seq
+          end
+        else
+          if comment.nil?
+            "@" + name + "\n" + seq + "\n+\n" + qual
+          else
+            "@" + name + " " + comment + "\n" + seq + "\n+\n" + qual
+          end
+        end
+      end
+    end
+  end
+end

lib/bio/kseq/version.rb

@@ -0,0 +1,5 @@
+module Bio
+  class Kseq
+    VERSION = "0.0.1"
+  end
+end

spec/seqtk_spec.rb → spec/kseq_spec.rb

@@ -1,6 +1,7 @@
-require 'bio/seqtk'
+require 'bio/kseq'
 require 'tempfile'
-include Bio::SeqTK
+
+include Bio
 
 describe Kseq do
   it 'should parse simple FASTA files' do
@@ -13,19 +14,19 @@
 
     kseq = Kseq.new tmp.path
 
-    expect(kseq.read!).to be_true
+    expect(kseq.read!).to be_truthy 
     expect(kseq.name).to eq("A")
     expect(kseq.comment).to be_nil
     expect(kseq.seq).to eq("AAAATTTTCCCCGGGG")
     expect(kseq.qual).to be_nil
 
-    expect(kseq.read!).to be_true
+    expect(kseq.read!).to be_truthy 
     expect(kseq.name).to eq("B")
     expect(kseq.comment).to eq("comment")
     expect(kseq.seq).to eq("GGGGTTTTCCCCAAAA")
     expect(kseq.qual).to be_nil
 
-    expect(kseq.read!).to be_false
+    expect(kseq.read!).to be_falsey
   end
 
   it 'should parse simple FASTQ files' do
@@ -42,19 +43,19 @@
 
     kseq = Kseq.new tmp.path
 
-    expect(kseq.read!).to be_true
+    expect(kseq.read!).to be_truthy
     expect(kseq.name).to eq("A")
     expect(kseq.comment).to be_nil
     expect(kseq.seq).to eq("AAAATTTTCCCCGGGG")
     expect(kseq.qual).to eq("AAAAAAAAAAAAAAAA")
 
-    expect(kseq.read!).to be_true
+    expect(kseq.read!).to be_truthy
     expect(kseq.name).to eq("B")
     expect(kseq.comment).to eq("comment")
     expect(kseq.seq).to eq("GGGGTTTTCCCCAAAA")
     expect(kseq.qual).to eq("IIIIIIIIIIIIIIII")
 
-    expect(kseq.read!).to be_false
+    expect(kseq.read!).to be_falsey
   end
 
   it 'should read from IO' do
@@ -69,18 +70,18 @@
 
     kseq = Kseq.new io
 
-    expect(kseq.read!).to be_true
+    expect(kseq.read!).to be_truthy
     expect(kseq.name).to eq("A")
     expect(kseq.comment).to be_nil
     expect(kseq.seq).to eq("AAAATTTTCCCCGGGG")
     expect(kseq.qual).to be_nil
 
-    expect(kseq.read!).to be_true
+    expect(kseq.read!).to be_truthy
     expect(kseq.name).to eq("B")
     expect(kseq.comment).to eq("comment")
     expect(kseq.seq).to eq("GGGGTTTTCCCCAAAA")
     expect(kseq.qual).to be_nil
 
-    expect(kseq.read!).to be_false
+    expect(kseq.read!).to be_falsey
   end
 end