--- a
+++ b/bin/mtx_to_adata.py
@@ -0,0 +1,136 @@
+"""
+Script for combining mtx files and its two corresponding metadata files into a anndata object.
+Does not do any normalization, but can handle some basic things like reindexing
+"""
+
+import os
+import sys
+from typing import *
+import argparse
+import logging
+
+import pandas as pd
+import anndata as ad
+from scipy.sparse import csr_matrix
+
+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 ensure_sane_interval(s: str, f: Callable = lambda x: x.split("_")) -> str:
+    """
+    Ensure that the atac interval follows format chr1:100-200
+    f is a function that maps input to a tuple of 3 parts
+    """
+    chrom, start, stop = f(s)
+    start = int(start)
+    stop = int(stop)
+    assert chrom.startswith("chr")
+    return f"{chrom}:{start}-{stop}"
+
+
+def build_parser():
+    """Build CLI parser"""
+    parser = argparse.ArgumentParser(
+        usage=__doc__, formatter_class=argparse.ArgumentDefaultsHelpFormatter
+    )
+    parser.add_argument("cell_info", type=str, help="File with cell metadata")
+    parser.add_argument(
+        "var_info", type=str, help="File with var (peak or gene) metadata"
+    )
+    parser.add_argument("mat_file", type=str, help="File with actual matrix of values")
+    parser.add_argument("out_h5ad", type=str, help="File to write output")
+    parser.add_argument(
+        "--cellindexcol",
+        type=int,
+        default=None,
+        help="Index column for cells. For ArchR output, this should be 0",
+    )
+    parser.add_argument(
+        "--varindexcol",
+        type=int,
+        default=None,
+        help="Index col for var. For ArchR output, this should be 5",
+    )
+    parser.add_argument(
+        "--reindexvar",
+        type=str,
+        default="",
+        help="File containing a list of variables that the outputted h5ad must adhere to",
+    )
+    parser.add_argument(
+        "--noheader",
+        action="store_true",
+        help="Do not consider the first line a header",
+    )
+    return parser
+
+
+def main():
+    """Run the script"""
+    parser = build_parser()
+    args = parser.parse_args()
+
+    cell_df = pd.read_csv(
+        args.cell_info,
+        delimiter=","
+        if utils.get_file_extension_no_gz(args.cell_info) == "csv"
+        else "\t",
+        index_col=args.cellindexcol,
+        header=None if args.noheader else "infer",  # 'infer' is default
+    )
+    if "Barcodes" in cell_df.columns and args.cellindexcol is not None:
+        cell_df.index = cell_df["Barcodes"]
+    cell_df.index = cell_df.index.rename("barcode")
+    cell_df.columns = cell_df.columns.map(str)
+
+    logging.info(f"Read cell metadata from {args.cell_info} {cell_df.shape}")
+    logging.info(f"Cell metadata cols: {cell_df.columns}")
+    logging.info(cell_df)
+
+    var_df = pd.read_csv(
+        args.var_info,
+        delimiter=","
+        if utils.get_file_extension_no_gz(args.var_info) == "csv"
+        else "\t",
+        index_col=args.varindexcol,
+        header=None if args.noheader else "infer",  # 'infer' is default
+    )
+    if "Feature" in var_df.columns and args.varindexcol is not None:
+        var_df.index = [ensure_sane_interval(s) for s in var_df["Feature"]]
+    var_df.index = var_df.index.rename("ft")
+    var_df.columns = var_df.columns.map(str)
+    # var_df.index = var_df.index.map(str)
+    logging.info(f"Read variable metadata from {args.var_info} {var_df.shape}")
+    logging.info(f"Var metadata cols: {var_df.columns}")
+    logging.info(var_df)
+
+    # Transpose because bio considers rows to be features
+    adata = ad.read_mtx(args.mat_file).T
+    logging.info(f"Read matrix {args.mat_file} {adata.shape}")
+    adata.obs = cell_df
+    adata.var = var_df
+    logging.info(f"Created AnnData object: {adata}")
+    logging.info(f"Obs names: {adata.obs_names}")
+    logging.info(f"Var names: {adata.var_names}")
+
+    if args.reindexvar:
+        assert args.varindexcol is not None, "Must provide var index col to reindex var"
+        target_vars = utils.read_delimited_file(args.reindexvar)
+        logging.info(f"Read {args.reindexvar} for {len(target_vars)} vars to reindex")
+        adata = adata_utils.reindex_adata_vars(adata, target_vars)
+
+    adata.X = csr_matrix(adata.X)
+    logging.info(f"Writing to {args.out_h5ad}")
+    adata.write_h5ad(args.out_h5ad, compression=None)
+
+
+if __name__ == "__main__":
+    main()