Usage

🚀 Quick start (CLI)

📁 Prepare input files

data/
├── drug_names.txt           # One drug per line
├── node_dict.csv            # Gene → Node mapping
└── synergy_data.csv         # Optional: drug combinations + effects

📝 Create config file

my_config.json:

{
  "global": {"output_dir": "results", "base_data_dir": "data"},
  "paths": {
    "drug_names_file": "drug_names.txt",
    "node_dict_file": "node_dict.csv",
    "synergy_data_file": "synergy_data.csv"
  },
  "options": {"double_drug_screen": true}
}

▶️ Run pipeline

# Full pipeline
drexpa --config my_config.json

# Generate profiles only
drexpa --config my_config.json --until profiles

# Specific steps
drexpa --config my_config.json --steps profiles,panel

# Verbose mode (structured logging + timing)
drexpa --config my_config.json --verbose

⌨️ CLI options

Option	Description	Example
--config PATH	Custom config JSON file	--config my_config.json
--synergy-data PATH	Override synergy data file	--synergy-data screen.csv
--output-dir DIR	Override output directory	--output-dir ./results
--until STEP	Run until step (inclusive)	--until panel
--steps STEPS	Specific steps (comma-separated)	--steps profiles,panel
--verbose	Enable structured logging + timing	--verbose

🔄 Pipeline steps

1. load_data — Load synergy data

2. chembl_ids — Resolve ChEMBL IDs (requires ChEMBL network access)

3. doses — Extract & process drug doses (requires concentration columns)

4. targets — Query internal drug-target database

5. node_targets — Map targets to logical model nodes

6. profiles — Generate unique drug profiles with Pipeline IDs

7. combinations — Prepare drug combinations (requires synergy data)

8. panel — Create drug panel (DrugLogics format)

9. perturbations — Generate perturbation files per condition

10. synergies — Process observed synergies

Dependencies are resolved automatically: --until panel runs steps 1–8 with all prerequisites.

🐍 Python API

from drexpa import run_pipeline

config = {
    "global": {"output_dir": "results"},
    "paths": {
        "drug_names_file": "data/drugs.txt",
        "node_dict_file": "data/nodes.csv",
    }
}

# Full pipeline
run_pipeline(config_dict=config)

# Specific steps
run_pipeline(
    config_dict=config,
    synergy_data_file="data/synergy.csv",
    steps_to_run=["profiles", "panel"],
)

📦 Output files

File	Step	Content
drug_ChEMBL_IDs.csv	chembl_ids	Drug name → ChEMBL ID mapping
drug_ChEMBL_doses.csv	doses	Drugs with IC50 concentrations
drug_ChEMBL_targets.csv	targets	Drug → Targets from database
drug_node_targets.csv	node_targets	Drug → Logical model nodes
drug_profiles.csv	profiles	Drug profiles with Pipeline IDs
drug_panel_df.csv	panel	Drug panel (DrugLogics format)
drugpanel	panel	Formatted drug panel file
<TISSUE>/	perturbations	Per-tissue perturbation files