[BioPython] Huge problems with examples

ssalie_lab_staff_health_med_uct at mail.med.uct.ac.za ssalie_lab_staff_health_med_uct at mail.med.uct.ac.za
Mon Jul 5 05:55:57 EDT 2004


Hi, I've downloaded Biopython onto windows XP and trying examples...quite a 
few error messages popping up when trying to run 

C:\>C:\Python23\examples\fasta_iterator.py
Traceback (most recent call last):
  File "C:\Python23\examples\fasta_iterator.py", line 29, in ?
    all_species = extract_organisms("ls_orchid.fasta")
  File "C:\Python23\examples\fasta_iterator.py", line 7, in extract_organisms
    file = open(file_to_parse, 'r')
IOError: [Errno 2] No such file or directory: 'ls_orchid.fasta'



C:\>C:\Examples\query_entrez.py
Traceback (most recent call last):
  File "C:\Examples\query_entrez.py", line 24, in ?
    doptcmdl = return_format)
  File "C:\Python23\Lib\site-packages\Bio\WWW\NCBI.py", line 51, in query
    return _open(cgi, variables)
  File "C:\Python23\Lib\site-packages\Bio\WWW\NCBI.py", line 191, in _open
    handle = urllib.urlopen(fullcgi)
  File "C:\Python23\lib\urllib.py", line 76, in urlopen
    return opener.open(url)
  File "C:\Python23\lib\urllib.py", line 181, in open
    return getattr(self, name)(url)
  File "C:\Python23\lib\urllib.py", line 297, in open_http
    h.endheaders()
  File "C:\Python23\lib\httplib.py", line 712, in endheaders
    self._send_output()
  File "C:\Python23\lib\httplib.py", line 597, in _send_output
    self.send(msg)
  File "C:\Python23\lib\httplib.py", line 564, in send
    self.connect()
  File "C:\Python23\lib\httplib.py", line 548, in connect
    raise socket.error, msg
IOError: [Errno socket error] (10060, 'Operation timed out')


C:\>C:\Python23\examples\fasta_consumer.py
Traceback (most recent call last):
  File "C:\Python23\examples\fasta_consumer.py", line 35, in ?
    all_species = extract_organisms("ls_orchid.fasta", 94)
  File "C:\Python23\examples\fasta_consumer.py", line 21, in extract_organisms
    scanner = Fasta._Scanner()
AttributeError: 'module' object has no attribute '_Scanner'


C:\>C:\Python23\examples\getgene.py
Traceback (most recent call last):
  File "C:\Python23\examples\getgene.py", line 36, in ?
    import gdbm
ImportError: No module named gdbm





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