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

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