scripts/4.aggregate.py
Aggregates single-cell profiles into guide-level and gene-level profiles per plate with Pycytominer, using operation (mean or median).
Does not respect overwrite_files.
Inputs¶
| Input | Description |
|---|---|
summary_data/{data_set_name}_sitelist.json | From step 2 |
single_cell/by_site/{plate}-{well}-{site}/*_single_cell.csv.gz | From step 2, when save_single_file is false |
single_cell/{plate}_single_cell_{data_set_name}.csv.gz | From step 2, when save_single_file is true |
Config used: data_sets (experiment); aggregate.*, process_SBS.gene_col, process_SBS.barcode_col, single_cell.save_single_file, core.* (defaults). See Configuration.
Outputs¶
| Output | Description |
|---|---|
profiles/{plate}_{data_set_name}_guide.csv.gz | One row per gene and barcode |
profiles/{plate}_{data_set_name}_gene.csv.gz | One row per gene |
Both have Metadata_Batch, Metadata_Plate, and Metadata_Dataset_Split added.