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bigbio / py-pgatk

Python tools for proteogenomics analysis toolkit
Apache License 2.0
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overlap between config parameters in cgenomes between cosmic and cbioportal downloaders #17

Closed husensofteng closed 3 years ago

husensofteng commented 5 years ago

refactoring is need for removing 'clinical_sample_file' from cosmic_config.yaml without breaking cosmic_to_proteindb in cgenomes_proteindb.py: https://github.com/bigbio/py-pgatk/blob/067aa7c90e8706559cc8cf841262920c3221f45c/pypgatk/cgenomes/cgenomes_proteindb.py#L18

to be removed: https://github.com/bigbio/py-pgatk/blob/067aa7c90e8706559cc8cf841262920c3221f45c/pypgatk/config/cosmic_config.yaml#L19

ypriverol commented 5 years ago

@husensofteng I have managed to move the project into Travis. Some minor changes has been done in the string format.

Can you let me know, what is this error you are mentioning here?

ypriverol commented 5 years ago

@husensofteng error in the test https://github.com/bigbio/py-pgatk/blob/364fdcdfe1c58a68370e431995c3b7a2cd963d8f/pypgatk/tests/pypgatk_tests.py#L155

husensofteng commented 5 years ago

the error is fixed. the issue was related to logger variables. they had to be moved into the class: here

husensofteng commented 5 years ago

@ypriverol if we could check we will close the issue.