gff3_assemble_spec.rb in bio-gff3-0.8.3

- old
+ new
@@ -75,21 +75,21 @@
   it "should translate CDS 7838:7980 (in frame 0, + strand)" do
     recs = @cdslist['cds:MhA1_Contig1133.frz3.gene4']
     component = @componentlist['cds:MhA1_Contig1133.frz3.gene4']
     cds0 = recs[0]
     cds0.seqname.should == 'MhA1_Contig1133'
-    seq = @gff.assemble(@contigsequence,component.start,[cds0])
+    seq = @gff.assemble(@contigsequence,component.start,[cds0],:trim=>false)
     seq.size.should == 143
     seq.should == "ATGCGTCCTTTAACAGATGAAGAAACTGAAAAGTTTTTCAAAAAACTTTCAAATTATATTGGTGACAATATTAAACTTTTATTGGAAAGAGAAGATGGAGAATATGTTTTTCGTTTACATAAAGACAGAGTTTATTATTGCAG"
     aaseq = @gff.assembleAA(@contigsequence,component.start,[cds0])
     aaseq.should == "MRPLTDEETEKFFKKLSNYIGDNIKLLLEREDGEYVFRLHKDRVYYC"
   end
   # MhA1_Contig1133	WormBase	CDS	8065	8308	.	+	1	ID=cds:MhA1_Contig1133.frz3.gene4;Parent=transcript:MhA1_Contig1133.frz3.gene4
   it "should translate CDS 8065:8308 (in frame 1, + strand)" do
     recs = @cdslist['cds:MhA1_Contig1133.frz3.gene4']
     component = @componentlist['cds:MhA1_Contig1133.frz3.gene4']
     cds1 = recs[1]
-    seq = @gff.assemble(@contigsequence,component.start,[cds1])
+    seq = @gff.assemble(@contigsequence,component.start,[cds1],:trim=>false)
     seq.size.should == 244
     seq.should == "TGAAAAATTAATGCGACAAGCAGCATGTATTGGACGTAAACAATTGGGATCTTTTGGAACTTGTTTGGGTAAATTCACAAAAGGAGGGTCTTTCTTTCTTCATATAACATCATTGGATTATTTGGCACCTTATGCTTTAGCAAAAATTTGGTTAAAACCACAAGCTGAACAACAATTTTTATATGGAAATAATATTGTTAAATCTGGTGTTGGAAGAATGAGTGAAGGGATTGAAGAAAAACAA"
     seq = @gff.assemble(@contigsequence,component.start,[cds1],:phase => true)
     seq.size.should == 243
     seq.should == "GAAAAATTAATGCGACAAGCAGCATGTATTGGACGTAAACAATTGGGATCTTTTGGAACTTGTTTGGGTAAATTCACAAAAGGAGGGTCTTTCTTTCTTCATATAACATCATTGGATTATTTGGCACCTTATGCTTTAGCAAAAATTTGGTTAAAACCACAAGCTGAACAACAATTTTTATATGGAAATAATATTGTTAAATCTGGTGTTGGAAGAATGAGTGAAGGGATTGAAGAAAAACAA"