--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fetch_cbioportal_data.py	Mon Apr 14 09:56:31 2025 +0000
@@ -0,0 +1,61 @@
+#!/usr/bin/env python
+
+import argparse
+import os
+
+from flexynesis.utils import CBioPortalData
+
+
+def main():
+    parser = argparse.ArgumentParser(description="Fetch and prepare cBioPortal data for Flexynesis.")
+    parser.add_argument("--study_id", required=True, help="cBioPortal study ID (e.g., 'brca_tcga')")
+    parser.add_argument("--data_types", required=True, help="Comma-separated list of data types (e.g., 'clin,mut,omics')")
+    parser.add_argument("--mapped_files", default=None, help="Comma-separated list of .txt files to map to data_types (optional)")
+    parser.add_argument("--split_ratio", type=float, default=0.7, help="Training/test split ratio (0.0 to 1.0)")
+    parser.add_argument("--output_dir", required=True, help="Output directory for datasets")
+
+    args = parser.parse_args()
+
+    data_types = args.data_types.split(",")
+    if "clin" not in data_types:
+        raise ValueError("Clinical data ('clin') is required for splitting the dataset.")
+
+    file_mapping = {
+        "clin": "data_clinical_patient.txt",  # can be any with 'clinical' in file name
+        "mut": "data_mutations.txt",  # any with 'mutations' in file name
+        "omics": "data_cna.txt",
+        "other": None
+    }
+
+    if args.mapped_files:
+        mapped_files = args.mapped_files.split(",")
+        if len(mapped_files) != len(data_types):
+            raise ValueError(f"Number of mapped files ({len(mapped_files)}) must match number of data types ({len(data_types)}).")
+        files_to_fetch = {dt: mf for dt, mf in zip(data_types, mapped_files)}
+        for mf in mapped_files:
+            if not mf.endswith(".txt"):
+                raise ValueError(f"Mapped file '{mf}' must end with '.txt'.")
+    else:
+        files_to_fetch = {dt: file_mapping[dt] for dt in data_types if dt in file_mapping}
+
+    invalid_types = set(data_types) - set(file_mapping.keys())
+    if invalid_types:
+        raise ValueError(f"Invalid data types: {invalid_types}. Supported types: {list(file_mapping.keys())}")
+
+    cbioportal = CBioPortalData(study_id=args.study_id)
+    cbioportal.get_cbioportal_data(study_id=args.study_id, files=files_to_fetch)
+    dataset = cbioportal.split_data(ratio=args.split_ratio)
+
+    os.makedirs(args.output_dir, exist_ok=True)
+
+    for data_type in data_types:
+        if data_type in dataset['train']:
+            train_file = os.path.join(args.output_dir, f"{data_type}_train.csv")
+            dataset['train'][data_type].to_csv(train_file, index=True)
+        if data_type in dataset['test']:
+            test_file = os.path.join(args.output_dir, f"{data_type}_test.csv")
+            dataset['test'][data_type].to_csv(test_file, index=True)
+
+
+if __name__ == "__main__":
+    main()