Skip to content

Error looking for .names property on zarr group  #137

Closed

Description

@alimanfoo

Cannot pass Zarr group into VariantChunkedTable constructor:

---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
<ipython-input-14-17c60e02130f> in <module>()
----> 1 variants_2L = allel.VariantChunkedTable(callset['2L/variants'])
      2 variants_2L

/home/aliman/miniconda3/envs/biipy240/lib/python3.5/site-packages/allel/model/chunked.py in __init__(self, data, names, index)
    814 
    815     def __init__(self, data, names=None, index=None):
--> 816         super(VariantChunkedTable, self).__init__(data, names=names)
    817         self.index = None
    818         if index is not None:

/home/aliman/miniconda3/envs/biipy240/lib/python3.5/site-packages/allel/chunked/core.py in __init__(self, data, names)
    804     # noinspection PyMissingConstructor
    805     def __init__(self, data, names=None):
--> 806         names, columns = _util.check_table_like(data, names=names)
    807         # skip super-class constructor because we are more flexible about type of values here
    808         self._values = data

/home/aliman/miniconda3/envs/biipy240/lib/python3.5/site-packages/allel/chunked/util.py in check_table_like(data, names)
     68         columns = list(data)
     69 
---> 70     elif hasattr(data, 'names'):
     71         # bcolz ctable or similar
     72         if names is None:

/home/aliman/miniconda3/envs/biipy240/lib/python3.5/site-packages/zarr/hierarchy.py in __getattr__(self, item)
    320     def __getattr__(self, item):
    321         # allow access to group members via dot notation
--> 322         return self.__getitem__(item)
    323 
    324     def group_keys(self):

/home/aliman/miniconda3/envs/biipy240/lib/python3.5/site-packages/zarr/hierarchy.py in __getitem__(self, item)
    302                          synchronizer=self._synchronizer)
    303         else:
--> 304             raise KeyError(item)
    305 
    306     def __setitem__(self, item, value):

KeyError: 'names'

Activity

  1. alimanfoo commented on Feb 27, 2017

    @alimanfoo
    ContributorAuthor

    This should be resolved in zarr 2.1.4 but should add a test to verify.

  2. modified the milestone: v1.1 on Jun 16, 2017
  3. added a commit that references this issue on Jun 19, 2017
    a6bfe43
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

      Milestone

      Relationships

      None yet

      Development

      No branches or pull requests

      Issue actions