Nokogiri XPath bug fix.

* Added .to_s to xpath method calls in #Bio::Blast::XPath.field to prevent gaps undefined method error when parsing Hsps.
pjotrp · Aug 8, 2012 · a3bfbe9 · a3bfbe9
1 parent 2642e84
commit a3bfbe9
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Showing 3 changed files with 4 additions and 2 deletions.
diff --git a/lib/bio/db/blast/parser/nokogiri.rb b/lib/bio/db/blast/parser/nokogiri.rb
@@ -8,9 +8,9 @@ module Blast
     module XPath
       def field name
         res = if @prefix
-          @xml.xpath(@prefix+name+'/text()')
+          @xml.xpath(@prefix+name+'/text()').to_s
         else
-          @xml.xpath(name+'/text()')
+          @xml.xpath(name+'/text()').to_s
         end
         if res == nil
           logger = Bio::Log::LoggerPlus['bio-blastxmlparser']

diff --git a/spec/bio-blastxmlparser_spec.rb b/spec/bio-blastxmlparser_spec.rb
@@ -43,6 +43,7 @@
     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 == "|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||"

diff --git a/test/data/nt_example_blastn.m7 b/test/data/nt_example_blastn.m7
@@ -46,6 +46,7 @@
               <Hsp_identity>73</Hsp_identity>
               <Hsp_positive>73</Hsp_positive>
               <Hsp_align-len>73</Hsp_align-len>
+              <Hsp_gaps>0</Hsp_gaps>
               <Hsp_qseq>AGTGAAGCTTCTAGATATTTGGCGGGTACCTCTAATTTTGCCTGCCTGCCAACCTATATGCTCCTGTGTTTAG</Hsp_qseq>
               <Hsp_hseq>AGTGAAGCTTCTAGATATTTGGCGGGTACCTCTAATTTTGCCTGCCTGCCAACCTATATGCTCCTGTGTTTAG</Hsp_hseq>
               <Hsp_midline>|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||</Hsp_midline>