bio-faster 0.4.2 → 0.4.3

data/VERSION

@@ -1 +1 @@
-0.4.2
+0.4.3

data/bio-faster.gemspec

@@ -5,7 +5,7 @@
 
 Gem::Specification.new do |s|
   s.name = "bio-faster"
-  s.version = "0.4.2"
+  s.version = "0.4.3"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Francesco Strozzi"]
@@ -75,7 +75,8 @@ Gem::Specification.new do |s|
     "test/data/formats/solexa_full_range_original_solexa.fastq",
     "test/data/formats/wrapping_as_illumina.fastq",
     "test/data/formats/wrapping_as_sanger.fastq",
-    "test/data/formats/wrapping_as_solexa.fastq"
+    "test/data/formats/wrapping_as_solexa.fastq",
+    "test/test_stdin.rb"
   ]
   s.homepage = "http://github.com/fstrozzi/bioruby-faster"
   s.licenses = ["MIT"]

data/ext/faster.c

@@ -8,7 +8,6 @@
 #include <stdlib.h>
 
 #define _BSIZE 100000
-
 typedef struct {
     char *id;
     char *seq;
@@ -67,8 +66,13 @@ int check_header(char *header, char *firstline) {
 int fastQ_iterator(FastQRecord *seq, int scale_factor) {
     // initialization of structure elements.
     char *header = "@"; // FastQ header
-    if (!seq->stream)
-      seq->stream = fopen(seq->filename,"r");
+    if (!seq->stream) {
+      if(strcmp(seq->filename,"stdin") == 0) {
+        seq->stream = stdin;
+      }  
+      else
+        seq->stream = fopen(seq->filename,"r");
+    }  
     if (!seq->line)
       seq->line = malloc(sizeof (char)* _BSIZE);
     if (!seq->bad_chars)
@@ -81,6 +85,7 @@ int fastQ_iterator(FastQRecord *seq, int scale_factor) {
     for (int i = 0; i < 4; i++)
     {
       if (fgets(seq->line, _BSIZE, seq->stream) == NULL) {
+        fclose(seq->stream);
         // if either sequence or quality is missing the record is truncated
         if((seq->seq != NULL && seq->raw_quality == NULL) || (seq->raw_quality != NULL && seq->seq == NULL)) return -2;
         else return 0;

data/lib/bio/faster.rb

@@ -33,7 +33,11 @@ module Bio
     attach_function :fastQ_iterator, [FastQRecord, :int], :int
 
     def each_record
-        raise ArgumentError, "File #{self.file} does not exist" unless File.exists? self.file
+        if self.file == :stdin
+          self.file = "stdin"
+        elsif !File.exists? self.file
+          raise ArgumentError, "File #{self.file} does not exist"
+        end
         record = FastQRecord.new
         scale_factor = nil
         case self.encoding

data/spec/parser_spec.rb

@@ -42,6 +42,41 @@ describe Bio::Faster do
 
     end
 
+    it "can read also gzipped FastQ files" do
+      gz_files = Dir.glob(TEST_DATA+"/formats/gzipped/*.fastq.gz").sort
+      gz_seq = []
+      gz_files.each do |file|
+        Bio::Faster.new(file).each_record do |seq|
+           gz_seq << seq
+        end    
+      end
+      files = Dir.glob(TEST_DATA+"/formats/gzipped/*.fastq").sort
+      norm_seq = []
+      files.each do |file|
+        Bio::Faster.new(file).each_record do |seq|
+           norm_seq << seq
+        end    
+      end
+      gz_seq.should == norm_seq
+    end
+
+
+    it "can read from the standard input" do
+      require 'digest/md5'
+      file = TEST_DATA+"/formats/illumina_full_range_as_illumina.fastq"
+      TEST = File.join(File.dirname(File.dirname(__FILE__)),"test")
+      system("cat "+file+" | ruby "+TEST+"/test_stdin.rb > stdin_test.out")
+      out = File.open("expected.out","w")
+      Bio::Faster.new(file).each_record do |seq|
+        out.write seq.to_s+"\n"
+      end
+      out.close()
+      md5_stdin = Digest::MD5.file("stdin_test.out")
+      md5_expected = Digest::MD5.file("expected.out")
+      md5_stdin.should == md5_expected
+      FileUtils.rm "stdin_test.out"
+      FileUtils.rm "expected.out"
+    end
 
   end
 

data/test/test_stdin.rb

@@ -0,0 +1,7 @@
+require File.join(File.dirname(File.dirname(__FILE__)),"spec","helper")
+
+stream = Bio::Faster.new :stdin
+stream.each_record do |seq|
+	print seq.to_s+"\n"
+end
+

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-faster
 version: !ruby/object:Gem::Version
-  version: 0.4.2
+  version: 0.4.3
   prerelease: 
 platform: ruby
 authors:
@@ -13,7 +13,7 @@ date: 2012-04-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
-  requirement: &2153396520 !ruby/object:Gem::Requirement
+  requirement: &2157623240 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *2153396520
+  version_requirements: *2157623240
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &2153396000 !ruby/object:Gem::Requirement
+  requirement: &2157622320 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -32,10 +32,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2153396000
+  version_requirements: *2157622320
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &2153395420 !ruby/object:Gem::Requirement
+  requirement: &2157621820 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -43,10 +43,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *2153395420
+  version_requirements: *2157621820
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &2153394940 !ruby/object:Gem::Requirement
+  requirement: &2157621200 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -54,10 +54,10 @@ dependencies:
         version: 1.6.4
   type: :development
   prerelease: false
-  version_requirements: *2153394940
+  version_requirements: *2157621200
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &2153394460 !ruby/object:Gem::Requirement
+  requirement: &2157620460 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -65,10 +65,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2153394460
+  version_requirements: *2157620460
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &2153393980 !ruby/object:Gem::Requirement
+  requirement: &2157619740 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -76,10 +76,10 @@ dependencies:
         version: 1.4.2
   type: :development
   prerelease: false
-  version_requirements: *2153393980
+  version_requirements: *2157619740
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &2153409780 !ruby/object:Gem::Requirement
+  requirement: &2157619000 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -87,10 +87,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2153409780
+  version_requirements: *2157619000
 - !ruby/object:Gem::Dependency
   name: ffi
-  requirement: &2153409260 !ruby/object:Gem::Requirement
+  requirement: &2157618200 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -98,7 +98,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2153409260
+  version_requirements: *2157618200
 description: A fast parser for FastQ files
 email: francesco.strozzi@gmail.com
 executables: []
@@ -166,6 +166,7 @@ files:
 - test/data/formats/wrapping_as_illumina.fastq
 - test/data/formats/wrapping_as_sanger.fastq
 - test/data/formats/wrapping_as_solexa.fastq
+- test/test_stdin.rb
 homepage: http://github.com/fstrozzi/bioruby-faster
 licenses:
 - MIT
@@ -181,7 +182,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 4125702484128053207
+      hash: -1208999662832865297
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: