[Biopython-dev] [Bug 2530] New: Bio.Seq.translate() treats invalid codons as stops
bugzilla-daemon at portal.open-bio.org
bugzilla-daemon at portal.open-bio.org
Sat Jun 28 20:09:44 UTC 2008
http://bugzilla.open-bio.org/show_bug.cgi?id=2530
Summary: Bio.Seq.translate() treats invalid codons as stops
Product: Biopython
Version: Not Applicable
Platform: All
OS/Version: All
Status: NEW
Severity: normal
Priority: P2
Component: Main Distribution
AssignedTo: biopython-dev at biopython.org
ReportedBy: biopython-bugzilla at maubp.freeserve.co.uk
The following results are with CVS. Biopython 1.45 may be different, I have
recently tweaked the translate function for some less dramatic issues.
I would like Bio.Seq.translate() to raise exceptions on untranslatable codons,
rather than inserting a stop character. e.g. for "N at N" or "TA-".
Currently:
>>> from Bio.Seq import translate
>>> translate("TAA")
'*'
>>> translate("TAG")
'*'
>>> translate("TAA")
'*'
>>> translate("TAC")
'Y'
>>> translate("TAN")
...
Bio.Data.CodonTable.TranslationError: 'TAN'
>>> translate("NNN")
...
Bio.Data.CodonTable.TranslationError: 'TAN'
>>> translate("AAA")
'K'
>>> translate("ANA")
'X'
>>> translate("AXA")
'X'
That is all fine. However,
>>> translate("A at A")
'*'
>>> translate("A-A")
'*'
These should also raise a TranslationError. Suggested non-trivial patch to
follow.
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