--- a
+++ b/bin/convert_to_BIRD_input.py
@@ -0,0 +1,71 @@
+"""
+Convert file to input format BIRD expects
+BIRD requires that genes are in the format ENSG00000236743.1
+"""
+# Example file: https://raw.githubusercontent.com/WeiqiangZhou/BIRD/master/example/FPKM_data_matrix.txt
+
+import os
+import sys
+import argparse
+import logging
+
+import numpy as np
+import pandas as pd
+import scanpy as sc
+import anndata as ad
+
+
+SRC_DIR = os.path.join(
+    os.path.dirname(os.path.dirname(os.path.abspath(__file__))), "babel"
+)
+assert os.path.isdir(SRC_DIR)
+sys.path.append(SRC_DIR)
+import adata_utils
+import utils
+
+logging.basicConfig(level=logging.INFO)
+
+
+def build_parser():
+    """Build CLI parser"""
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        "input",
+        type=str,
+        help="Input file to convert. Should be of gene expression",
+    )
+    parser.add_argument("output_table_txt", type=str, help="File to write")
+    parser.add_argument(
+        "--transforms", default="", required=False, type=str, choices=["log1p", "exp"]
+    )
+    return parser
+
+
+def main():
+    parser = build_parser()
+    args = parser.parse_args()
+
+    _, input_ext = os.path.splitext(args.input)
+    if input_ext == ".h5ad":
+        x = ad.read_h5ad(args.input)
+    elif input_ext == ".h5":
+        x = sc.read_10x_h5(args.input)
+    else:
+        raise ValueError(f"Unrecognized file extension: {args.input}")
+    logging.info(f"Read input: {x}")
+
+    logging.info("Reading gtf for gene name map")
+    gene_name_map = utils.read_gtf_gene_symbol_to_id()
+
+    # Tranpose because BIRD wants features x obs
+    x_df = pd.DataFrame(utils.ensure_arr(x.X), index=x.obs_names, columns=x.var_names).T
+    assert np.all(x_df.values >= 0.0)
+    x_df.index = [gene_name_map[g] for g in x_df.index]
+
+    # Write output (tab-separated table
+    logging.info(f"Writing output to {args.output_table_txt}")
+    x_df.to_csv(args.output_table_txt, sep="\t")
+
+
+if __name__ == "__main__":
+    main()