[Biopython] error in parseing Gene bank

francesco chiani francesco.chiani at gmail.com
Wed Oct 3 14:18:22 UTC 2012


Hi Everyone,
Someone have an idea of why in biopython  for python 2.7 give me this error
while parsing a gene bank file?


Traceback (most recent call last):
in <module>
    for seq_record in SeqIO.parse(handle, "genbank"):
  File "C:\Python27\lib\site-packages\Bio\SeqIO\__init__.py", line 537, in parse
    for r in i:
  File "C:\Python27\lib\site-packages\Bio\GenBank\Scanner.py", line 445, in
parse_records
    record = self.parse(handle, do_features)
  File "C:\Python27\lib\site-packages\Bio\GenBank\Scanner.py", line 428, in parse
    if self.feed(handle, consumer, do_features):
  File "C:\Python27\lib\site-packages\Bio\GenBank\Scanner.py", line 410, in feed
    consumer.record_end("//")
  File "C:\Python27\lib\site-packages\Bio\GenBank\__init__.py", line 1184, in
record_end
    % self._seq_type)
ValueError: Could not determine alphabet for seq_type dna

p.s.-:This doesn't happen in biopython for python 2.6 version I suppose, 'cause
with the same gene bank file in this version my script works...


thanks x your help,
F.




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