Hi Chris,
I am testing the script again and getting these error message. I checked out
pygr 5 hours ago.
==> my scripts.
myslices = pygr.Data.Collection(filename = os.path.join(wDir, 'gccontents',
'reference_gc.cdb'), \
intKeys = True, mode = 'c', writeback = False)
mydb = seqdb.AnnotationDB(myslices, hg18, sliceAttrDict = dict(id = 0, gc_id
= 1, orientation = 2, start = 3, \
stop = 4, gc_content = 5))
==> all error and warning messages.
Warning: you opened shelve file
/Genome1/deepreds/gccontents/reference_gc.cdb
in mode 'c' but this is ambiguous for how the shelve should be
re-opened later during unpickling. By default it will be
re-opened in mode 'r' (read-only). To make it be re-opened
writable, create it in mode 'cw', or call its method
reopen('w'), which will make it be re-opened in mode 'w' now and
in later unpickling. To suppress this warning message, use the
verbose=False option.
Traceback (most recent call last):
File "make_pygr_annotation_gccontents.py", line 23, in <module>
stop = 4, gc_content = 5))
File
"/home/deepreds/lib/python2.5/site-packages/pygr-0.7-py2.5-linux-x86_64.egg/pygr/seqdb.py",
line 819, in __init__
sample_value = self.itervalues().next()
StopIteration
WARNING: saving pygr.Data pending data that you forgot to save...
Remember in the future, you must issue the command pygr.Data.save() to save
your pending pygr.Data resources to your resource database(s), or
alternatively
pygr.Data.rollback() to dump those pending data without saving them.
It is a very bad idea to rely on this automatic attempt to save your
forgotten data, because it is possible that the Python interpreter
may never call this function at exit (for details see the atexit module
docs in the Python Library Reference).
Yours,
Namshin Kim
On Fri, Sep 12, 2008 at 3:15 AM, Christopher Lee <[EMAIL PROTECTED]> wrote:
>
>
> On Sep 11, 2008, at 4:19 AM, Namshin Kim wrote:
>
> > First thing is maxlen and maxint is not working in
> > cnestedlist.NLMSA. I calculated and set the max idb size to be 1GB,
> > but it grows upto 4GB and stopped due to a memory error. Memory
> > error is caused by excessive memory usage in Collection.
> > seqdb.AnnotationDB.clear() function does not exist any more. I
> > reported this excessive memory usage in shelve and AFAIK
> > writeback=False option would prevent excessive memory usage. Please
> > let me know if I made a mistake.
>
> Hi Namshin,
> I think we need to disentangle the several possibilities that you
> mentioned:
> - maxlen, maxint size control of the NLMSA idb. Nothing has changed
> in this code and I doubt that this is the cause of your problem. Is
> the idb file actually growing above the max size you specified, or was
> your 4GB number simply a measure of RAM usage? Your report didn't
> make that clear.
>
> - Collection, which is just a shelve interface. Since you're using
> writeback=False it seems Collection is probably not the problem. Once
> again, nothing has changed in this code.
>
> - seqdb.AnnotationDB.clear(): as Titus said, he removed this
> recently. But we don't know whether you tested this with that most
> recent version. Actually, since your code example uses the clear()
> method, that implies you must be using an earlier version of Pygr.
> Please give us the git commit ID of the code that suffers the problem
> you reported.
>
> Please file this as a bug report in the issue tracker. See my recent
> email on what information I would like included in the report...
>
> It would also be helpful if you could re-test this problem with
> different pygr versions:
> - the latest git repository code: AnnotationDB by default now has a
> new option autoGC=True which automatically frees any annotation
> objects that the user is not currently using. Hopefully this will
> solve your problem.
> - if that doesn't solve the problem, please report to us the most
> recent version that does NOT have the memory usage problem you are
> reporting.
>
> Thanks!!!
>
> -- Chris
>
> >
>
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