[BioPython] GenBank parsing

[Kyle Dent]

Dear All,

My script was successfully implementing the Genbank
parser until just today I was trying to get it to
parse a genpept file. After much experimentation I
discovered that it was actually having trouble parsing
even newly downloaded GenBank files as well
(downloaded of NCBI).

I wanted to ask if anyone is aware of this problem, I
understand the flat file format was updated this month
and is probably the cause of this.

The output which I am getting:

Traceback (most recent call last):
  File "C:\work\GB CDS Extractor.py", line 289, in
open1_clicked
    loadGenBank(self, self.gbFilePath)
  File "C:\work\GB CDS Extractor.py", line 75, in
loadGenBank
    cur_record = genBank_Iterator.next()
  File
"C:\Python24\Lib\site-packages\Bio\GenBank\__init__.py",
line 129, in nex
t
    return self._parser.parse(File.StringHandle(data))
  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
356, in parseStrin
g
    self._err_handler.fatalError(result)
  File "C:\Python24\lib\xml\sax\handler.py", line 38,
in fatalError
    raise exception
Martel.Parser.ParserPositionException: error parsing
at or beyond character 136

With thanks,
Kyle


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