Second half of pipeline + plotting - Githubissues

Arcadia-Science / ProteinCartography

a pipeline to build similarity maps of protein space

MIT License

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Second half of pipeline + plotting #17

Closed mezarque closed 1 year ago

mezarque commented 1 year ago

With apologies to the reviewers, this PR builds out the second half of the Snakemake pipeline, including a bunch of additional functions and scripts:

downloading files from AlphaFold
pulling metadata from Uniprot
performing Foldseek all-v-all tmscore and clustering
generating various features files for plotting
aggregating features files
performing dimensionality reduction
interactive plotting with Plotly
3d visualization in Jupyter notebooks with py3dmol

As well as some QOL stuff:

passing parameters through the pipeline using a config file
deleted extraneous notebooks
tidied up unnecessary files

The revised rulegraph looks like this:

This PR does not yet address the following issues, which will be built into (much smaller) PRs following this one.

separating out conda environments for each rule
creating --local flags for all (or most) API queries
setting up test databases

I've also tagged @elizabethmcd as she'll be helping to make the pipeline Nextflow-ized in the medium term.

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