[Biopython-dev] [Bug 3098] New: GenBank/EMBL parser breaks for between features at origin

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Thu Jun 10 18:18:41 UTC 2010


           Summary: GenBank/EMBL parser breaks for between features at
           Product: Biopython
           Version: 1.54
          Platform: PC
        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

I was testing Bio.SeqIO with with a GenBank file gbpln1.seq which includes:

LOCUS       AB042240              134545 bp    DNA     circular PLN 02-MAY-2006
     misc_feature    134545^1
                     /note="Junction IRA-LSC"

This is a "between" feature of length zero at the origin of this circular
genome. This is a special case since normally between positions "start^end"
have end=start+1 (using one based counting) which the parser does not allow

The same applies to EMBL files as well, e.g.

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