[Biopython-dev] GenBank parsing problem

[Chunlei Wu]

Another GenBank parsing problem when parsing "S40706",
which seems also related with "linear".

>>> from Bio import GenBank
>>> gi=GenBank.search_for('S40706')[0]
>>>
ncbi_dict=GenBank.NCBIDictionary(parser=GenBank.FeatureParser())
>>> ncbi_dict[gi]
Traceback (most recent call last):
  File "<interactive input>", line 1, in ?
  File "C:\Python21\Bio\GenBank\__init__.py", line
1555, in __getitem__
    return self.parser.parse(handle)
  File "C:\Python21\Bio\GenBank\__init__.py", line
268, in parse
    self._scanner.feed(handle, self._consumer)
  File "C:\Python21\Bio\GenBank\__init__.py", line
1250, in feed
    self._parser.parseFile(handle)
  File "C:\Python21\Martel\Parser.py", line 247, in
parseFile
    self.parseString(fileobj.read())
  File "C:\Python21\Martel\Parser.py", line 283, in
parseString
    self._cont_handler.endDocument()
  File "C:\Python21\Bio\ParserSupport.py", line 311,
in endDocument
    self._make_callback(self._previous_tag)
  File "C:\Python21\Bio\ParserSupport.py", line 300,
in _make_callback
    callback_function(info_to_pass)
  File "C:\Python21\Bio\GenBank\__init__.py", line
984, in record_end
    raise ValueError("Could not determine alphabet for
seq_type %s"
ValueError: Could not determine alphabet for seq_type
linear


Chunlei 



--- Brad Chapman <chapmanb at arches.uga.edu> wrote:
> Hi Chunlei;
> 
> >     Thank you for your fix. But it seems I can not
> get
> > the latest version of genbank_format.py from CVS.
> The
> > current one is still the old one ver. 1.16. Maybe
> some
> > delay of the server?
> 
> Hmm, you're right. It still is 1.16. The anonymous
> CVS normally syncs up
> with the read/write access CVS in a few hours, so
> maybe something is
> wrong with anonymous CVS (most of the administrators
> are having fun in
> the sun in Arizona right now). 
> 
> Anyways, until the fix moves to anonymous CVS, you
> can grab the changed
> file from:
> 
>
http://www.bioinformatics.org/bradstuff/bp/genbank_format-1.17.py
> 
> Sorry about the pain!
> Brad
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev at biopython.org
> http://biopython.org/mailman/listinfo/biopython-dev


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