[Biopython-dev] [Bug 3175] New: Caret in genbank files leads to GenBank Parser crash in Biopython 1.54

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

http://bugzilla.open-bio.org/show_bug.cgi?id=3175

           Summary: Caret in genbank files leads to GenBank Parser crash in
                    Biopython 1.54
           Product: Biopython
           Version: 1.54
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: major
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: aaron.tin.long.lun at gmail.com


When parsing genbank files using Bio.SeqIO as described in the Biopython
Cookbook, the presence of a caret in the position of a feature in the
annotation (e.g. CDS   1000..1001^1002) raises a LocationParserError, leading
to "Syntax error at or near `Tokens('caret')' token". Appears to occur
regardless of the type of the feature, whether it is normal/reverse complement,
etc. Found in BioPython 1.54 on a Dell dimension 2400 running Kubuntu 10.10.


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