dna 0.0.10 → 0.0.11

data/dna.gemspec

@@ -1,6 +1,6 @@
 Gem::Specification.new do |s|
 	s.name    = 'dna'
-	s.version = '0.0.10'
+	s.version = '0.0.11'
 	s.date    = '2012-05-21'
 
 	s.summary     = 'DNA sequence parser'

data/lib/dna.rb

@@ -1,3 +1,5 @@
+require 'zlib'
+
 Dir.glob(File.join(File.dirname(__FILE__), 'parsers', '*.rb')).each { |f| require f }
 
 ##
@@ -25,6 +27,16 @@ class Dna
   end
 
   def detect_format
+    
+    # is gzipped?
+    unless @handle.class == Array # for tests mostly...
+      begin
+        @handle = Zlib::GzipReader.new(@handle)
+      rescue
+        @handle.rewind
+      end
+    end
+    
     first_line = @handle.first
     @handle.rewind if @handle.class == File
 

data/readme.md

@@ -23,7 +23,7 @@ With Ruby 1.8.7 or better:
 DNA gem has grep-like capabilities. Print records with (Ruby) regexp match in header.
 
 ```
-$ dna input.fastq "[1-2]"
+$ dna spec/data/input.fastq "[1-2]"
 
 @1
 TGAAACTTATTGATCACCCCGCTTGGCGTTGGGGAGAAATTCAGAAAAGAGTGCTTGATGGGGCGCCACATGCCGTGCAACCCACTCTCTTTCACGCAGCGCGCCCCA
@@ -34,7 +34,7 @@ GTCGCGGCTTACCACCCAACGATTTTTTTTAGAGGTGCTGGTTTCA
 +2
 2550//*-1./4.--/'+.2.,,,,,,,,&(/00.11426554+13
 
-$ cat input.fasta | dna "\d"
+$ dna spec/data/test.fasta "\d"
 
 >1
 GAGAGATCTCATGACACAGCCGAAG
@@ -72,4 +72,14 @@ File.open('sequences.qseq') do |handle|
   records = Dna.new handle
   puts records.first.inspect
 end
+
+# even works on gzipped data
+
+File.open('sequences.fasta.gz') do |handle|
+  records = Dna.new handle
+
+  records.each do |record|
+    puts record.length
+  end
+end
 ```

data/spec/dna_spec.rb

@@ -7,11 +7,16 @@ describe Dna do
   let(:fastq) { Dna.new @fastq_file }
   let(:qseq) { Dna.new @qseq_file }
   let(:empty) { Dna.new @empty_file }
+  let(:gzipped) { Dna.new @gzip_file }
 
   it 'doesnt freak out on empty files' do
     fasta.format == :empty
   end
 
+  it 'can automatically parse gzipped files' do
+    gzipped.format.should == :fasta
+  end
+
   it 'can auto-detect fasta format' do
     fasta.format.should == :fasta
   end

data/spec/spec_helper.rb

@@ -14,6 +14,7 @@ shared_context "parser stuff" do
     @fasta_file = fasta_file
     @fastq_file = fastq_file
     @qseq_file = qseq_file
-    @empty_fiel = empty_file
+    @empty_file = empty_file
+    @gzip_file = File.open(File.join(path, 'data/test.fasta.gz'))
   end
 end

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: dna
 version: !ruby/object:Gem::Version 
-  hash: 11
+  hash: 9
   prerelease: 
   segments: 
   - 0
   - 0
-  - 10
-  version: 0.0.10
+  - 11
+  version: 0.0.11
 platform: ruby
 authors: 
 - Austin G. Davis-Richardson
@@ -39,6 +39,7 @@ files:
 - readme.md
 - spec/data/empty.txt
 - spec/data/test.fasta
+- spec/data/test.fasta.gz
 - spec/data/test.fastq
 - spec/data/test.qseq
 - spec/dna_spec.rb
@@ -80,6 +81,7 @@ summary: DNA sequence parser
 test_files: 
 - spec/data/empty.txt
 - spec/data/test.fasta
+- spec/data/test.fasta.gz
 - spec/data/test.fastq
 - spec/data/test.qseq
 - spec/dna_spec.rb