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

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