And I optimized the prepare_entity_binding_ratios.py script to reduce the memory usage. The main changes are:
needs to be changed (impact on runtime)
Additionally:
fixed a bug in the computation of entity-wise binding ratios
If we add more such scripts for downstream analysis, one needs to think how to efficiently do this. In anyway one needs to keep the data model in mind to avoid creating too huge dataframes. One can also think about a script to extract the required tables for multiple plots in one step, similar to what AntoniaSchuster did.
In general, for this it might make sense to consider what type of other downstream analyses might be of interest here.
PR checklist
[ ] This comment contains a description of changes (with reason).
[ ] If you've fixed a bug or added code that should be tested, add tests!
[ ] If you've added a new tool - have you followed the pipeline conventions in the contribution docs
[ ] If necessary, also make a PR on the nf-core/metapep branch on the nf-core/test-datasets repository.
[ ] Make sure your code lints (nf-core lint).
[ ] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
[ ] Usage Documentation in docs/usage.md is updated.
[ ] Output Documentation in docs/output.md is updated.
[ ] CHANGELOG.md is updated.
[ ] README.md is updated (including new tool citations and authors/contributors).
And I optimized the
prepare_entity_binding_ratios.pyscript to reduce the memory usage. The main changes are:Additionally:
If we add more such scripts for downstream analysis, one needs to think how to efficiently do this. In anyway one needs to keep the data model in mind to avoid creating too huge dataframes. One can also think about a script to extract the required tables for multiple plots in one step, similar to what AntoniaSchuster did. In general, for this it might make sense to consider what type of other downstream analyses might be of interest here.
PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).