[Biopython-dev] [Bug 2894] New: Jython List difference causes failed assertion in CondonTable Fix+Patch

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2894

           Summary: Jython List difference causes failed assertion in
                    CondonTable Fix+Patch
           Product: Biopython
           Version: 1.51b
          Platform: Other
        OS/Version: Other
            Status: NEW
          Severity: enhancement
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: kellrott at ucsd.edu


Different list behaviour in Jython causes assertion to fail because last to
elements on produced list are swapped.  Haven't taken the time to figure out if
this caused by sloppy list usage or Jython list weirdness.  At this point, will
assume that list order doesn't matter and simple expand the assertion to allow
both cases...

list_ambiguous_codons(['TGA', 'TAA', 'TAG'],IUPACData.ambiguous_dna_values) 
Python : ['TGA', 'TAA', 'TAG', 'TAR', 'TRA']
Jython : ['TGA', 'TAA', 'TAG', 'TRA', 'TAR']

NOTE: Fixing this bug causes setup.py to fail (java.lang.ClassFormatError:
Invalid method Code length) because it exposes previously untested bugs 

*** biopython-1.51b_orig/Bio/Data/CodonTable.py 2009-05-08 14:20:19.000000000
-0700
--- biopython-1.51b/Bio/Data/CodonTable.py      2009-08-01 13:30:46.000000000
-0700
***************
*** 615,621 ****
  assert list_ambiguous_codons(['TAG', 'TGA'],IUPACData.ambiguous_dna_values)
== ['TAG', 'TGA']
  assert list_ambiguous_codons(['TAG', 'TAA'],IUPACData.ambiguous_dna_values)
== ['TAG', 'TAA', 'TAR']
  assert list_ambiguous_codons(['UAG', 'UAA'],IUPACData.ambiguous_rna_values)
== ['UAG', 'UAA', 'UAR']
! assert list_ambiguous_codons(['TGA', 'TAA',
'TAG'],IUPACData.ambiguous_dna_values) == ['TGA', 'TAA', 'TAG', 'TAR', 'TRA']

  # Forward translation is "onto", that is, any given codon always maps
  # to the same protein, or it doesn't map at all.  Thus, I can build
--- 615,623 ----
  assert list_ambiguous_codons(['TAG', 'TGA'],IUPACData.ambiguous_dna_values)
== ['TAG', 'TGA']
  assert list_ambiguous_codons(['TAG', 'TAA'],IUPACData.ambiguous_dna_values)
== ['TAG', 'TAA', 'TAR']
  assert list_ambiguous_codons(['UAG', 'UAA'],IUPACData.ambiguous_rna_values)
== ['UAG', 'UAA', 'UAR']
! #Jython BUG? For some order Jython swaps the order of the last two
elements...
! assert list_ambiguous_codons(['TGA', 'TAA',
'TAG'],IUPACData.ambiguous_dna_values) == ['TGA', 'TAA', 'TAG', 'TAR', 'TRA']
or\
!       list_ambiguous_codons(['TGA', 'TAA',
'TAG'],IUPACData.ambiguous_dna_values) == ['TGA', 'TAA', 'TAG', 'TRA', 'TAR']

  # Forward translation is "onto", that is, any given codon always maps
  # to the same protein, or it doesn't map at all.  Thus, I can build


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