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

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

http://bugzilla.open-bio.org/show_bug.cgi?id=3098

           Summary: GenBank/EMBL parser breaks for between features at
                    origin
           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
                     /standard_name="JLA"
                     /note="Junction IRA-LSC"
ORIGIN 
...

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
for.

The same applies to EMBL files as well, e.g.
http://www.ebi.ac.uk/cgi-bin/expasyfetch?AB042240


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