gff3_assemble3_spec.rb in bio-gff3-0.8.3

- old
+ new

@@ -28,11 +28,10 @@
       @cdslist[id] = reclist
     end
     name = "cds:MhA1_Contig1040.frz3.gene"
     recs = @cdslist[name]
     component = @componentlist[name]
-    p recs
     ntseq = @gff.assemble(@contigsequence,component.start,recs,:raw=>true)
     ntseq.should == "TTAATTAATTTGCCTAGAAAAACAAAGGCATAACATGCTTGCAGTCATCATACGGTAAGAGAGAAACCAACGATATGTTAATAATGTTGATGGGGGAATATCCTCATTAGAATTCTTTTTTGGGTGAATTGAAATTGCCATATTATTAGTATTATTAGAAAATATTAAATTTGTTGATAA"
     ntseq = @gff.assemble(@contigsequence,component.start,recs,:codonize=>true)
     ntseq.should == "TTATCAACAAATTTAATATTTTCTAATAATACTAATAATATGGCAATTTCAATTCACCCAAAAAAGAATTCTAATGAGGATATTCCCCCATCAACATTATTAACATATCGTTGGTTTCTCTCTTACCGTATGATGACTGCAAGCATGTTATGCCTTTGTTTTTCTAGGCAAATTAATTAA"
     aaseq = @gff.assembleAA(@contigsequence,component.start,recs)
@@ -53,9 +52,29 @@
     # ntseq.should == ""
     ntseq = @gff.assemble(@contigsequence,component.start,recs,:codonize=>true)
     ntseq.should == "AAAATTAATAAAAAAATAAATGATAATTCTTTTAATATTCAATCTGATTCGAATGAAAATTTGTTTAATGATGGAATTAATTCTGAACAAAATGAAGACAATATAGCAACAAAAAAAGGCAACAAAAAATTCGGTAAAAATCAAAAAGAAGGAAATAAAGAGTTGGATATTCAAAGTGAAGGTTTTGATAATAATGAAATACCTTCAAAAGAAAGCAAAAAACAAATAAGTAATTTTGGGGATAATGAAAGTGAATATGAAAAAGAAGAGGATAATAGAAAAAAGAAAGGGAAAAAAGGAATGATAGAAAAGTATGAATTAGGAAGGAATAAAGGAAGGGATAAAAATGAAAGAAATAAGGCTTCTGAAAGGTTTGATGAGCAGAATCAAGACAGAAATAATCAACGTGATAGTTTTGATTCTGGCAATAATGATAAATCACAAAGAGGCTTAGATAGCGGCACATTAGATGGAACAAATAATTTAAAAAGATCGAATGATGATCAATTACCAGAATTTTTGAAAACGGCCAGTCTCTCAGAGCGTCAGAAATTTCTTCAACTTGAAGCAGAAAATGACAGGTCCAAGTCTTCTATACGAAGAGATAAACAGAATTGGGCTGATCAACAAGGGCAGAGAATTTCTGATCTTTATAAACAATTTCAACAATCTTTACAACAAAAAGAAAAACAATTTAAAAGTGAACGTCAACGAAATGTTCAAATTAAATTAAGCAGAAATGCACAGAATGTTGATAAAAGAATTCAGGATCTTCTGAATAATCCTGATATTGCTGAAAGAGCTTTAATTCTTCAAATTGAACAAATCCTCGGCGGTACAGACGATAGTATTCGTCAGGAATTACAAAGACAAATATCTGTTATTGGACCATTAGATGGAAATATACCGCCAAATCTTACATAG"
     aaseq = @gff.assembleAA(@contigsequence,component.start,recs)
     aaseq.should == "KINKKINDNSFNIQSDSNENLFNDGINSEQNEDNIATKKGNKKFGKNQKEGNKELDIQSEGFDNNEIPSKESKKQISNFGDNESEYEKEEDNRKKKGKKGMIEKYELGRNKGRDKNERNKASERFDEQNQDRNNQRDSFDSGNNDKSQRGLDSGTLDGTNNLKRSNDDQLPEFLKTASLSERQKFLQLEAENDRSKSSIRRDKQNWADQQGQRISDLYKQFQQSLQQKEKQFKSERQRNVQIKLSRNAQNVDKRIQDLLNNPDIAERALILQIEQILGGTDDSIRQELQRQISVIGPLDGNIPPNLT*"
+  end
+  it "should fix Wormbase error MhA1_Contig3426.frz3.gene1" do
+    @contigsequence = @gff.sequencelist["MhA1_Contig3426"]
+    @componentlist = {}
+    @cdslist = {}
+    @gff.each_CDS do | id, reclist, component |
+      @componentlist[id] = component
+      @cdslist[id] = reclist
+    end
+    name = "cds:MhA1_Contig3426.frz3.gene1"
+    recs = @cdslist[name]
+    component = @componentlist[name]
+    # :raw should not fix
+    ntseq = @gff.assemble(@contigsequence,component.start,recs,:raw=>true)
+    ntseq.should == "GCATCCAACAACAACAATTAGAAGTCTTTCCCAGCTCCTCCTCTGCCCCTCAGCAACAACAATACCCAGCGCAGCAGCTTCAATTAGTTACTCCTTTTATTGCATGCATAGCAGATGAATTGAGGGAGTTGATAGATGAAATGCGTATGTTTTAG"
+    ntseq = @gff.assemble(@contigsequence,component.start,recs,:codonize=>true,:fix=>true)
+    ntseq.should == "ATCCAACAACAACAATTAGAAGTCTTTCCCAGCTCCTCCTCTGCCCCTCAGCAACAACAATACCCAGCGCAGCAGCTTCAATTAGTTACTCCTTTTATTGCATGCATAGCAGATGAATTGAGGGAGTTGATAGATGAAATGCGTATGTTTTAG"
+    ntseq.size.should == 153
+    aaseq = @gff.assembleAA(@contigsequence,component.start,recs,:fix=>true)
+    aaseq.should == "IQQQQLEVFPSSSSAPQQQQYPAQQLQLVTPFIACIADELRELIDEMRMF*"
   end
 end
 
 
 