TypeError: annotate() got an unexpected keyword argument 'regions'

[manburst]

Hello just try genmod by using example file and got this error

cat examples/test_vcf.vcf |\

genmod annotate - --annotate-regions |\ genmod models - --family_file examples/recessive_trio.ped > test_vcf_models_annotated.vcf

Traceback (most recent call last): File "/home/staff/anaconda3/bin/genmod", line 33, in <module> sys.exit(load_entry_point('genmod==3.8.0', 'console_scripts', 'genmod')()) File "/home/staff/anaconda3/lib/python3.9/site-packages/click/core.py", line 722, in __call__ return self.main(*args, **kwargs) File "/home/staff/anaconda3/lib/python3.9/site-packages/click/core.py", line 697, in main rv = self.invoke(ctx) File "/home/staff/anaconda3/lib/python3.9/site-packages/click/core.py", line 1066, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/staff/anaconda3/lib/python3.9/site-packages/click/core.py", line 895, in invoke return ctx.invoke(self.callback, **ctx.params) File "/home/staff/anaconda3/lib/python3.9/site-packages/click/core.py", line 535, in invoke return callback(*args, **kwargs) File "/home/staff/anaconda3/lib/python3.9/site-packages/click/decorators.py", line 17, in new_func return f(get_current_context(), *args, **kwargs) TypeError: annotate() got an unexpected keyword argument 'regions' Traceback (most recent call last): File "/home/staff/anaconda3/bin/genmod", line 33, in <module> sys.exit(load_entry_point('genmod==3.8.0', 'console_scripts', 'genmod')()) File "/home/staff/anaconda3/lib/python3.9/site-packages/click/core.py", line 722, in __call__ return self.main(*args, **kwargs) File "/home/staff/anaconda3/lib/python3.9/site-packages/click/core.py", line 697, in main rv = self.invoke(ctx) File "/home/staff/anaconda3/lib/python3.9/site-packages/click/core.py", line 1066, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/staff/anaconda3/lib/python3.9/site-packages/click/core.py", line 895, in invoke return ctx.invoke(self.callback, **ctx.params) File "/home/staff/anaconda3/lib/python3.9/site-packages/click/core.py", line 535, in invoke return callback(*args, **kwargs) File "/home/staff/anaconda3/lib/python3.9/site-packages/click/decorators.py", line 17, in new_func return f(get_current_context(), *args, **kwargs) File "/home/staff/anaconda3/lib/python3.9/site-packages/genmod-3.8.0-py3.9.egg/genmod/commands/annotate_models.py", line 171, in models UnboundLocalError: local variable 'line' referenced before assignment

Noted that there were some errors when I installed it with pip. However, I can still call the 'genmod' command. But, when I tried the command, I got the same error as mentioned above. So, I uninstalled it and installed it with setup.py instead. Now, there are no errors showing during the installation, but I still get the same error result at the end when I use the example command.

Thank in advance

[jemten]

Also experienced this error and the 3.8.1 release seems to have fixed that particular issue

[torbjorgen]

Solved in 3.8.1.