oncotree_to_oncotree.py should support python3

cBioPortal / oncotree

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Closed thomasyu888 closed 3 years ago

thomasyu888 commented 4 years ago

fixes #212 This was run with python 3.7.6

urllib.urlopen is no longer a thing in python3. It is urllib.request.urlopen
DeprecationWarning: 'U' mode is deprecated (It is the default in python3)
```
with open(file, "rU"):
```
oncotree_code = lists_of_all_ancestors[0][min_length - 1]
```
TypeError: 'dict_values' object is not subscriptable
```
TypeError: unsupported operand type(s) for >>: 'builtin_function_or_method' and '_io.TextIOWrapper'. Did you mean "print(<message>, file=<output_stream>)"

thomasyu888 commented 4 years ago

Not sure why the tests are failing, but would be happy to fix.

thomasyu888 commented 4 years ago

@sheridancbio . Thoughts of this?

sheridancbio commented 3 years ago

This work has been incorporated into the master branch (with adjustments) via PR #233