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.egg/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.egg/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.egg/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.egg/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.egg/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.egg/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.