scripts/5.normalize.py
Normalizes each plate’s guide-level and gene-level profiles with Pycytominer.
Columns that are all 0 are dropped, and location columns are not normalized.
Normalization statistics are calculated from the samples in by_samples (by default the control_genes).
Inputs¶
| Input | Description |
|---|---|
profiles/{plate}_{data_set_name}_{gene|guide}.csv.gz | From step 4 |
Config used: data_sets, control_genes (experiment); normalize.*, process_SBS.gene_col, core.* (defaults). See Configuration.
Outputs¶
| Output | Description |
|---|---|
profiles/{plate}_{data_set_name}_{gene|guide}_normalized.csv.gz | Normalized profiles |
single_cell/single_cell_by_gene/{data_set_name}_{gene|guide}_normalized_{gene}.csv.gz | The normalized profiles split into one file per gene (only if output_bygene is true) |
If no samples match by_samples for a plate (e.g. no control gene is present), a warning is logged and that plate is not normalized.