scbi_fastq 0.0.19 → 0.0.21

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: 2ae8b1289a1b80610dac9e517dbcb98403f542a5
+  metadata.gz: f7c70741d511792ef974608199e0a4ec299957a2
+  data.tar.gz: 5890ced565c6a6d459e9e8ff7efe8ca644117085
 SHA512:
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+  metadata.gz: 4b06320c47f291320c78ea1c5ddce2553e2a6e860549bb47b1dbf456119015d871eed993b281dcc2cecd5def97ca32773c6b3c06ae887c6ae2ce91c61161c07d
+  data.tar.gz: b0a2bb95fe5a37e07f3febfcc4b95034f9d83bce5d78d62c08e6fd5b44076bb5401507a5aa38cc34c3eeef3a2e1e87e1d5e60fa19a58a5786bd6b296ed5e64b9

data/lib/scbi_fastq/fastq_file.rb

@@ -1,5 +1,5 @@
 require 'zlib'
-require 'scbi_multi_gz_reader'
+require 'scbi_zcat'
 
 # add ord method to ruby 1.8
 if !String.instance_methods.include?(:ord)
@@ -42,11 +42,12 @@ class FastqFile
       if fasta_file_name.is_a?(IO)
         @fastq_file = fasta_file_name
       else
-        begin
+        if ScbiZcatFile.gz_file?(fasta_file_name)
           #@fastq_file = Zlib::GzipReader.open(fasta_file_name)
-          @fastq_file = MultiGzReader.new(fasta_file_name)
+          #@fastq_file = MultiGzReader.new(fasta_file_name)
+          @fastq_file = ScbiZcatFile.new(fasta_file_name)
           # puts "GZIP file detected"
-        rescue => e
+        else
           @fastq_file = File.open(fasta_file_name,'r')
           # puts "NORMAL file detected"
         end

data/lib/scbi_fastq/version.rb

@@ -1,3 +1,3 @@
 module ScbiFastq
-  VERSION = "0.0.19"
+  VERSION = "0.0.21"
 end

data/scbi_fastq.gemspec

@@ -18,7 +18,7 @@ Gem::Specification.new do |spec|
   spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
   spec.require_paths = ["lib"]
 
-  spec.add_runtime_dependency "scbi_multi_gz_reader"
+  spec.add_runtime_dependency "scbi_zcat", ">= 0.0.1"
   spec.add_development_dependency "bundler", "~> 1.7"
   spec.add_development_dependency "rake", "~> 10.0"
 end

data/test/scbi_fastq_test.rb

@@ -30,48 +30,8 @@ class TestScbiFastq < Test::Unit::TestCase
 
     fqr.close
 
-
   end
 
-
-  def test_mini_multi_gz_reader
-
-    file=MultiGzReader.new(File.join(File.dirname(__FILE__),'minitest.fastq.gz'))
-    
-    i=0
-
-    loop do
-      res=file.readline
-      #puts "LINE: #{res}"
-      break if res.nil?
-      i=i+1
-    end
-
-    file.close
-
-    assert_equal(i,28)
-
-  end
-
-  def test_mini_multi_gz_reader_EOF_while
-
-    # test a file with multiple gz streams
-
-    fqr=FastqFile.new(File.join(File.dirname(__FILE__),'minitest.fastq.gz'))
-    
-    i=0
-
-    fqr.each do |n,s,q|
-      if !n.nil?
-        i+=1
-      end
-    end
-
-    fqr.close
-
-    assert_equal(7,i)
-
-  end
   
   def fill_file(n,offset=33)
     f=FastqFile.new(@test_file,'w')
@@ -207,6 +167,8 @@ class TestScbiFastq < Test::Unit::TestCase
   end
 
 
+
+
   def fill_file_gz(n,offset=33)
     f=FastqFile.new(@test_file_gz,'w.gz')
     puts "FILE GZ"
@@ -259,4 +221,30 @@ class TestScbiFastq < Test::Unit::TestCase
   #   fq.close
   #
   # end
+
+   def test_each_large
+
+    # make new file and fill with data
+    #fill_file(100)
+
+
+    fqr=FastqFile.new('/tmp/pair2.fastq.gz')
+
+    i=1
+
+    fqr.each do |n,s,q|
+      puts n
+      #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(40,i)
+      
+
+    fqr.close
+  end
+
 end

metadata

@@ -1,29 +1,29 @@
 --- !ruby/object:Gem::Specification
 name: scbi_fastq
 version: !ruby/object:Gem::Version
-  version: 0.0.19
+  version: 0.0.21
 platform: ruby
 authors:
 - dariogf
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-12-03 00:00:00.000000000 Z
+date: 2015-07-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
-  name: scbi_multi_gz_reader
+  name: scbi_zcat
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 0.0.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 0.0.1
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement