Error: AttributeError: 'generator' object has no attribute 'items'

Issue #28 new
Former user created an issue

Hello, I am getting this error when running oncodrivefml. I have oncodrive version 2.1.3 and am running it in a python 3.6 environment. My environment has bgparsers v. 0.9 and pytabix v. 0.0.2.

Traceback (most recent call last):
  File "/dir/oncodrivefml_3_6/bin/oncodrivefml", line 11, in <module>
    sys.exit(cmdline())
  File "/dir/oncodrivefml_3_6/lib/python3.6/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "/dir/oncodrivefml_3_6/lib/python3.6/site-packages/click/core.py", line 782, in main
    rv = self.invoke(ctx)
  File "/dir/oncodrivefml_3_6/lib/python3.6/site-packages/click/core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/dir/oncodrivefml_3_6/lib/python3.6/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/dir/oncodrivefml_3_6/lib/python3.6/site-packages/oncodrivefml/main.py", line 104, in cmdline
    override_config)
  File "/dir/oncodrivefml_3_6/lib/python3.6/site-packages/oncodrivefml/main.py", line 56, in main
    analysis.run()
  File "/dir/oncodrivefml_3_6/lib/python3.6/site-packages/oncodrivefml/oncodrivefml.py", line 189, in run
    save_pickle=self.generate_pickle)
  File "/dir/oncodrivefml_3_6/lib/python3.6/site-packages/oncodrivefml/load.py", line 230, in load_and_map_variants
    elements_tree = load_elements_tree(elements_file)
  File "/dir/oncodrivefml_3_6/lib/python3.6/site-packages/bgcache/decorator.py", line 81, in new_function
    cached_value = old_function(input_file)
  File "/dir/oncodrivefml_3_6/lib/python3.6/site-packages/oncodrivefml/load.py", line 181, in load_elements_tree
    return build_regions_tree(elements)
  File "/dir/oncodrivefml_3_6/lib/python3.6/site-packages/oncodrivefml/load.py", line 164, in build_regions_tree
    for i, (k, allr) in enumerate(regions.items()):
AttributeError: 'generator' object has no attribute 'items'

Comments (1)

  1. Iker Reyes

    Seems a problem between bgparsers and OncodriveFML versions. Either update FML, or downgrade bgparsers (to 0.7)

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