Created
November 12, 2021 18:04
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python3 ontobio/io/differ.py --file1 /tmp/noctua_mgi-src.gpad --file2 /tmp/noctua_mgi-src.gpad --output /tmp/test.b.out --group_by_column DB_Object_ID --group_by_column Evidence_type
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(env) sjcarbon@moiraine:~/local/src/git/ontobio[gpad_differ]$:( python3 ontobio/io/differ.py --file1 /tmp/noctua_mgi-src.gpad --file2 /tmp/noctua_mgi-src.gpad --output /tmp/test.b.out --group_by_column DB_Object_ID --group_by_column Evidence_type | |
/home/sjcarbon/local/src/git/ontobio/env/lib/python3.7/site-packages/rdflib_jsonld/__init__.py:12: DeprecationWarning: The rdflib-jsonld package has been integrated into rdflib as of rdflib==6.0.1. Please remove rdflib-jsonld from your project's dependencies. | |
DeprecationWarning, | |
Traceback (most recent call last): | |
File "ontobio/io/differ.py", line 354, in <module> | |
compare_files() | |
File "/home/sjcarbon/local/src/git/ontobio/env/lib/python3.7/site-packages/click/core.py", line 1128, in __call__ | |
return self.main(*args, **kwargs) | |
File "/home/sjcarbon/local/src/git/ontobio/env/lib/python3.7/site-packages/click/core.py", line 1053, in main | |
rv = self.invoke(ctx) | |
File "/home/sjcarbon/local/src/git/ontobio/env/lib/python3.7/site-packages/click/core.py", line 1395, in invoke | |
return ctx.invoke(self.callback, **ctx.params) | |
File "/home/sjcarbon/local/src/git/ontobio/env/lib/python3.7/site-packages/click/core.py", line 754, in invoke | |
return __callback(*args, **kwargs) | |
File "ontobio/io/differ.py", line 45, in compare_files | |
df_file1, df_file2, assocs1, assocs2 = get_parser(file1, file2) | |
File "ontobio/io/differ.py", line 198, in get_parser | |
df_file1, parser1 = get_typed_parser(file1_obj, file1) | |
File "ontobio/io/differ.py", line 181, in get_typed_parser | |
df_file = read_gpad_csv(filename, parser.version) | |
File "ontobio/io/differ.py", line 243, in read_gpad_csv | |
if version.startswith("1"): | |
AttributeError: 'NoneType' object has no attribute 'startswith' |
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