Hi Naomi, What Python version are you using? Do a python -V from the comand line (note that capital V)!
Cheers, Steve On Dec 21, 8:21 am, Naomi Ellen <naomi.r.el...@gmail.com> wrote: > Hi, > > I recently installed pygr-0.8.2-py2.6-macosx-10.6-universal.egg. > > When I was trying to construct sequence objects from a fasta file, I ran > into the following error: > > >>> from pygr import seqdb > >>> sp = seqdb.SequenceFileDB('/Users/naomi/projects/data/MM2235/MM2235.fa') > > WARNING dbfile.open_index: Falling back to hash index: unable to import > bsddb > DEBUG seqdb._create_seqLenDict: Building sequence length index... > WARNING dbfile.open_index: Falling back to hash index: unable to import > bsddb > Traceback (most recent call last): > File "<stdin>", line 1, in <module> > File > "/Library/Python/2.6/site-packages/pygr-0.8.2-py2.6-macosx-10.6-universal.e > gg/pygr/seqdb.py", > line 433, in __init__ > SequenceDB.__init__(self, filepath=filepath, dbname=dbname, **kwargs) > File > "/Library/Python/2.6/site-packages/pygr-0.8.2-py2.6-macosx-10.6-universal.e > gg/pygr/seqdb.py", > line 232, in __init__ > self._set_seqtype() > File > "/Library/Python/2.6/site-packages/pygr-0.8.2-py2.6-macosx-10.6-universal.e > gg/pygr/seqdb.py", > line 244, in _set_seqtype > for seqID in self: # get an iterator > File > "/Library/Python/2.6/site-packages/pygr-0.8.2-py2.6-macosx-10.6-universal.e > gg/pygr/seqdb.py", > line 304, in __iter__ > return iter(self.seqInfoDict) > File > "/Library/Python/2.6/site-packages/pygr-0.8.2-py2.6-macosx-10.6-universal.e > gg/pygr/seqdb.py", > line 517, in __iter__ > return iter(self.seqDB.seqLenDict) > File > "/Library/Python/2.6/site-packages/pygr-0.8.2-py2.6-macosx-10.6-universal.e > gg/pygr/dbfile.py", > line 150, in __iter__ > Original error message was: %s''' % str(exc_value)) > TypeError: cannot iterate over this dictionary. > This means that you do not have bsddb, bsddb3, or gdbm available for use by > the 'shelve' module in this Python install. Please fix this! > > Original error message was: 'dbm.dbm' object is not iterable > > Could you suggest how to proceed? > > Thanks, > Naomi -- You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to pygr-...@googlegroups.com. To unsubscribe from this group, send email to pygr-dev+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en.