[Biopython-dev] [Bug 2887] New: set iteration order dependency in Bio.Data.CodonTable

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Mon Jul 27 14:48:55 UTC 2009


           Summary: set iteration order dependency in Bio.Data.CodonTable
           Product: Biopython
           Version: 1.51b
          Platform: PC
        OS/Version: Windows
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: fwereade at googlemail.com

Running under IronPython 2.0.1 with ironclad r515
(http://code.google.com/p/ironclad )

    from Bio.Data import CodonTable
  File "C:\dev\biopython-1.51b\Bio\Data\CodonTable.py", line 618, in
    assert list_ambiguous_codons(['TGA', 'TAA',
'TAG'],IUPACData.ambiguous_dna_values) == ['TGA', 'TAA', 'TAG', 'TAR', 'TRA']

cause: set iteration order is different in IronPython (it may also be different
in Jython and/or PyPy, and has the potential to change across CPython versions)

fix: make Bio.Data.CodonTable.py:618 read as follows

assert set(list_ambiguous_codons(['TGA', 'TAA',
'TAG'],IUPACData.ambiguous_dna_values)) == set(['TGA', 'TAA', 'TAG', 'TAR',

better fix: as above, but for all similar lines (the preceding lines currrently
work under ipy)

just a thought: it might also be worth moving all the tests into the Tests
directory, rather than running them inline every time.

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