[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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