Major review to the code

bigbio / py-pgatk

Python tools for proteogenomics analysis toolkit

Apache License 2.0

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Major review to the code #8

Closed ypriverol closed 3 years ago

ypriverol commented 5 years ago

@yafeng :

I have made all the changes requested, the current version of the library contains two new commands:

cosmic-to-proteindb
cbioportal-to-proteindb

I have removed the scripts from the DB folder. The last thing is missing is for you to review some of the code comments of variables that are not use:

https://github.com/bigbio/py-pgatk/blob/master/cgenomes/cgenomes_proteindb.py#L95

When you finish let me know !!!

yafeng commented 5 years ago

Done! commits pushed.

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