gff3_assemble3_spec.rb in bio-gff3-0.8.5

- old
+ new

@@ -10,14 +10,14 @@
 
 include Bio::GFFbrowser
 
 GFF3FILE3="test/data/gff/test-cds.gff3"
 
-describe GFFdb, "Assemble CDS (extra checks)" do
+describe GFF3, "Assemble CDS (extra checks)" do
   before :all do 
-    gffdb = Bio::GFFbrowser::GFFdb.new(GFF3FILE3)
-    @gff = gffdb.assembler
+    gff3 = Bio::GFFbrowser::GFF3.new(GFF3FILE3)
+    @gff = gff3.assembler
     @gff.parse
   end
 
   it "should translate gene MhA1_Contig1040.frz3.gene29" do
     @contigsequence = @gff.sequencelist["MhA1_Contig1040"]
@@ -25,10 +25,10 @@
     @cdslist = {}
     @gff.each_CDS do | id, reclist, component |
       @componentlist[id] = component
       @cdslist[id] = reclist
     end
-    name = "cds:MhA1_Contig1040.frz3.gene"
+    name = "cds:MhA1_Contig1040.frz3.gene29"
     recs = @cdslist[name]
     component = @componentlist[name]
     ntseq = @gff.assemble(@contigsequence,component.start,recs,:raw=>true)
     ntseq.should == "TTAATTAATTTGCCTAGAAAAACAAAGGCATAACATGCTTGCAGTCATCATACGGTAAGAGAGAAACCAACGATATGTTAATAATGTTGATGGGGGAATATCCTCATTAGAATTCTTTTTTGGGTGAATTGAAATTGCCATATTATTAGTATTATTAGAAAATATTAAATTTGTTGATAA"
     ntseq = @gff.assemble(@contigsequence,component.start,recs,:codonize=>true)