[Biopython-dev] [Bug 2597] New: Enforce alphabet letters in Seq objects

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2597

           Summary: Enforce alphabet letters in Seq objects
           Product: Biopython
           Version: Not Applicable
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: enhancement
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: biopython-bugzilla at maubp.freeserve.co.uk
 BugsThisDependsOn: 2532


If a Seq object is created with an alphabet with a pre-defined set of letters
(e.g. the IUPAC alphabets) then I think Biopython should validate that the
sequence does indeed only use those letters.

This will catch mis-use of ambiguous sequences with non-ambiguous alphabets,
letters in an unexpected case, and most importantly any unexpected symbols
(e.g. from a parsing problem).

This will impose a performance overhead - which can be avoided if the user
instead chooses to use a generic dna/rna/protein alphabet which does not list
the letters expected.

Note that we will have to resolve Bug 2532 before doing this, as currently some
parts of Biopython are mis-using the upper case only IUPAC alphabet objects
with mixed case sequences.


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