diff pyscenic_binarize_aucell.py @ 0:31a8c822882f draft default tip

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6f7bc53bd9da7ee2a480b5aa2d1825209738c4c4

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyscenic_binarize_aucell.py	Sun Sep 15 10:13:34 2024 +0000
@@ -0,0 +1,50 @@
+import argparse
+
+import pandas as pd
+from pyscenic.binarization import binarize
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Binarize AUC matrix")
+    parser.add_argument("input_file", help="Input TSV or CSV file")
+    parser.add_argument(
+        "--threshold-overrides",
+        type=str,
+        help="Threshold overrides in JSON format",
+    )
+    parser.add_argument("--seed", type=int, default=None, help="Random seed")
+    parser.add_argument(
+        "--num-workers", type=int, default=1, help="Number of workers"
+    )
+    parser.add_argument(
+        "--output-prefix", type=str, default="output", help="Output prefix"
+    )
+
+    args = parser.parse_args()
+
+    # Read input file
+    if args.input_file.endswith(".tsv"):
+        auc_mtx = pd.read_csv(args.input_file, sep="\t", index_col=0)
+    elif args.input_file.endswith(".csv"):
+        auc_mtx = pd.read_csv(args.input_file, index_col=0)
+    else:
+        raise ValueError("Input file must be a TSV or CSV file")
+
+    auc_mtx.apply(pd.to_numeric)
+    # Parse threshold overrides
+    threshold_overrides = None
+    if args.threshold_overrides:
+        import json
+
+        threshold_overrides = json.loads(args.threshold_overrides)
+
+    # Call binarize function
+    binarized_mtx, thresholds = binarize(
+        auc_mtx, threshold_overrides, args.seed, args.num_workers
+    )
+
+    # set column name for thresholds
+    thresholds.rename("threshold", inplace=True)
+
+    # Save output files
+    binarized_mtx.to_csv(f"{args.output_prefix}/binarized_mtx.tsv", sep="\t")
+    thresholds.to_csv(f"{args.output_prefix}/thresholds.tsv", sep="\t")