[Biopython-dev] [Bug 2446] New: Comments in CT tags cause Bio.Sequencing.Ace.ACEParser to fail.

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2446

           Summary: Comments in CT tags cause Bio.Sequencing.Ace.ACEParser
                    to fail.
           Product: Biopython
           Version: Not Applicable
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: dthomp325 at gmail.com


When parsing an ace file that contains CT tags with comments such as those
added by Polyphred 6.11, Bio.Sequencing.Ace.ACEParser appears to get stuck in
an infinite loop until it dies with a memory usage exception.

example CT tag with comment:
CT{
Contig36 polyPhredRank1 polyPhred 3608 3608 080205:125543
COMMENT{
99
C}
}

Parsing works correctly for the exact same ace file minus the COMMENTs.


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