dna 0.0.3 → 0.0.4

data/lib/dna.rb

@@ -57,7 +57,7 @@ class Dna # iterator
         n = c.next
         case n
         when 0
-          params[:name] = line.strip
+          params[:name] = line.strip[1..-1]
         when 1
           params[:sequence] = line.strip
         when 2
@@ -143,7 +143,7 @@ class QSEQ < Record
   def initialize(args={})
     # These are the properties defined by the qseq spec
     # they must be in the same order that they appear in the tab-separated qseq file
-
+    @properties = :machine, :run, :lane, :tile, :x, :y, :index, :read_no, :sequence, :quality, :filtered
     @machine = args[:machine]
     @run = args[:run]
     @lane = args[:lane]

data/spec/dna_spec.rb

@@ -7,16 +7,18 @@ describe Dna do
   let (:fastq) { Dna.new @fastq_file, format: 'fastq' }
   let (:qseq) { Dna.new @qseq_file, format: 'qseq' }
 
-  it 'can parse a crappily formatted fasta file' do
-    fasta.to_a.length.should == 2
+  it 'can properly parse a crappily formatted fasta file' do
+    records = fasta.to_a
+    records[1].name.should == '2'
   end
 
   it 'generates fasta objects from a fasta file' do
     fasta.first.class.should == Fasta
   end
 
-  it 'can parse fastq format' do
-    fastq.to_a.length.should == 2
+  it 'can properly parse fastq format' do
+    records = fastq.to_a
+    records[1].name.should == '2'
   end
 
   it 'generates fastq objects from a fasta file' do
@@ -27,8 +29,9 @@ describe Dna do
     fastq.first.sequence.should_not be_nil
   end
 
-  it 'can parse qseq' do
-    qseq.to_a.length.should == 2
+  it 'can properly parse qseq format' do
+    records = qseq.to_a
+    records[1].sequence.should == 'GTGTGCCAGCAGCCGCGGTAATACAGAGGGGGCAAGCGTTGTTCGGAATTACTGGGCGTAAAGGGCGCGTAGGCGGCCCGCTAAGCCGAACGTGAAATCCC'
   end
 
   it 'generates qseq objects from a qseq file' do

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: dna
 version: !ruby/object:Gem::Version
-  version: 0.0.3
+  version: 0.0.4
   prerelease: 
 platform: ruby
 authors: