[Biopython-dev] [Bug 2410] New: DBSeq & DBSeqRecord should subclass Seq & SeqRecord

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Mon Nov 26 20:57:42 UTC 2007


           Summary: DBSeq & DBSeqRecord should subclass Seq & SeqRecord
           Product: Biopython
           Version: 1.44
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: BioSQL
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: biopython-bugzilla at maubp.freeserve.co.uk

The DBSeq and DBSeqRecord classes are defined in BioSQL/BioSeq.py

They attempt to implement the core API defined for the corresponding objects in
Bio.Seq and Bio.SeqRecord, via database wrappers which load and caches data on
demand.  The idea being that the DBSeqRecord and DBSeq can be used
interchangeably with the classic SeqRecord with Seq.

The problem is they are lacking several useful methods including __str__ and
__repr__ (see changes made to the Seq object on Bug 2351) and other Seq object
methods like count, complement and reverse_complement (see also enhancement Bug

I propose to make DBSeq and DBSeqRecord subclass Seq and SeqRecord
respectively.  Trivial patch to follow - the two BioSQL unit tests seem to pass
just fine.

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