bio-blastxmlparser_spec.rb in bio-blastxmlparser-1.1.0

- old
+ new

@@ -1,11 +1,11 @@
 require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
 
 TESTFILE = "./test/data/nt_example_blastn.m7"
+include Bio::Blast
 
 describe "Bio::Blast::NokogiriBlastXml" do
-  include Bio::Blast
   before(:all) do
     n = NokogiriBlastXml.new(File.new(TESTFILE)).to_enum
     @iter1 = n.next
     @iter2 = n.next
   end
@@ -41,9 +41,10 @@
     hsp.query_frame.should == 1
     hsp.hit_frame.should == 1
     hsp.identity.should == 73
     hsp.positive.should == 73
     hsp.align_len.should == 73
+    hsp.gaps.should == 0
     hsp.qseq.should == "AGTGAAGCTTCTAGATATTTGGCGGGTACCTCTAATTTTGCCTGCCTGCCAACCTATATGCTCCTGTGTTTAG"
     hsp.hseq.should == "AGTGAAGCTTCTAGATATTTGGCGGGTACCTCTAATTTTGCCTGCCTGCCAACCTATATGCTCCTGTGTTTAG"
     hsp.midline.should == "|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||"
     @iter2.iter_num.should == 2
     hits = @iter2.hits.first(3)