Error: AttributeError: 'generator' object has no attribute 'items'
Issue #28
new
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'
Seems a problem between bgparsers and OncodriveFML versions. Either update FML, or downgrade bgparsers (to 0.7)