[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
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.
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