Implementation of RFC64: 'mutational signatures' in the backend

[MatthijsPon]

Implementation of RFC#64 in the backend

Describe changes proposed in this pull request:

• Addition of a standalone scripts which takes in a study path and generates mutational signature files following RFC64.
• Mutational matrices are constructed from a maf file in the given study path.
• Create mutational signature contributions and P-values per COSMIC signature using MSKCC's tempoSig.

TODO's:

• Possible implementation of other mutational signature algorithms
• Convert count matrices to generic assay files and create accompanying meta files
• No test created yet, validateData.py needs to be extended

Checks

• Runs on heroku
• Has tests or has a separate issue that describes the types of test that should be created. If no test is included it should explicitly be mentioned in the PR why there is no test.
• The commit log is comprehensible. It follows 7 rules of great commit messages. For most PRs a single commit should suffice, in some cases multiple topical commits can be useful. During review it is ok to see tiny commits (e.g. Fix reviewer comments), but right before the code gets merged to master or rc branch, any such commits should be squashed since they are useless to the other developers. Definitely avoid merge commits, use rebase instead.
• Is this PR adding logic based on one or more clinical attributes? If yes, please make sure validation for this attribute is also present in the data validation / data loading layers (in backend repo) and documented in File-Formats Clinical data section!

[SRodenburg]

Very nice start, I proposed some minor restructuring to make the code more intuitive.

I feel like we should move the temposig outside of the script, and let the user give an installation directory.

Another thing, I discourage the removal of directories in the script. Just make clear in the names of the generated tmp files that they are temporary.

[sonarqubecloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
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0 Code Smells

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[pvannierop]

Mutational Signatures Backend

[SRodenburg]

Nice work Matthijs,

Some code suggestions and a few spots where I think we can improve on clarity, structure or efficiency, as indicated.

It would be nice to add these scripts in a subfolder mutational_signatures to keep this together.
Also, how can we work with the SigProfiler package in the Docker image?

[MatthijsPon]

Implementation moved to cbioportal/datahub-study-curation-tools: PR#48