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

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2887

           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 )

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

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',
'TRA'])
---------------------------------------------

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.


-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.