[Biopython-dev] [Bug 1909] New: Format issue with GenBank with segmented BACs (eg GI:55276707)

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

http://bugzilla.open-bio.org/show_bug.cgi?id=1909

           Summary: Format issue with GenBank with segmented BACs (eg
                    GI:55276707)
           Product: Biopython
           Version: Not Applicable
          Platform: PC
        OS/Version: Windows
            Status: NEW
          Severity: blocker
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: moscou at iastate.edu


When using the FeatureParser, it will not be able to retrieve this function. 
The following is the error message from BioPython.  I am assuming this is
because this BAC was kept together because of repetitive regions that could not
be resolved, but still represent different sequences.  Instead I am just going
skip this record for now.


55276707
Traceback (most recent call last):
  File "search_ncbi_for_barley_bacs.py", line 43, in ?
    gb_seqrecord = ncbi_dict[gi]
  File "C:\Python24\Lib\site-packages\Bio\GenBank\__init__.py", line 1364, in
__
getitem__
    return self.parser.parse(handle)
  File "C:\Python24\Lib\site-packages\Bio\GenBank\__init__.py", line 219, in
par
se
    self._scanner.feed(handle, self._consumer)
  File "C:\Python24\Lib\site-packages\Bio\GenBank\__init__.py", line 1259, in
fe
ed
    self._parser.parseFile(handle)
  File "C:\Python24\Lib\site-packages\Martel\Parser.py", line 328, in parseFile
    self.parseString(fileobj.read())
  File "C:\Python24\Lib\site-packages\Martel\Parser.py", line 361, in
parseStrin
g
    self._err_handler.fatalError(ParserIncompleteException(pos))
  File "C:\Python24\lib\xml\sax\handler.py", line 38, in fatalError
    raise exception
Martel.Parser.ParserIncompleteException: error parsing at or beyond character
18
263 (unparsed text remains)


Thanks a lot!




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