Merge branch 'dev' of https://github.com/pinellolab/crispr-bean into …

…main

bean/framework/read_from_csvs.py

@@ -0,0 +1,60 @@
+import argparse
+
+from perturb_tools._readwrite._funcs._read_screen_from_csvs import read_csvs
+from perturb_tools import Screen
+
+
+def get_input_parser() -> argparse.Namespace:
+    """Add multi-sample specific arguments to the base parser."""
+    print(
+        r"""
+    _ _       
+  /  \ '\                      _        
+  |   \  \     __ _ _ ___ __ _| |_ ___ 
+   \   \  |   / _| '_/ -_) _` |  _/ -_)
+    `.__|/    \__|_| \___\__,_|\__\___|
+    """
+    )
+    parser = argparse.ArgumentParser(
+        description="bean-create-screen parameters",
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+    )
+    parser.add_argument(
+        "gRNA_info_table_csv",
+        type=str,
+        help="Path to gRNA info .csv table, with index at first column and column names at the first row.",
+    )
+    parser.add_argument(
+        "samples_info_table_csv",
+        type=str,
+        help="Path to sample info .csv table, with index at first column and column names at the first row.",
+    )
+    parser.add_argument(
+        "gRNA_counts_table_csv",
+        type=str,
+        help="Path to gRNA counts .csv table, with index at first column and column names at the first row.",
+    )
+    parser.add_argument(
+        "-e",
+        "--edits",
+        type=str,
+        help="Path to edit counts .csv table, with index at first column and column names at the first row.",
+        default=None,
+    )
+    parser.add_argument(
+        "-o",
+        "--output-prefix",
+        type=str,
+        help="Output file prefix (output will be saved as `output_prefix.h5ad`). If not provided, `gRNA_counts_table_csv` file prefix is used.",
+        default=None,
+    )
+    return parser
+
+
+def create_screen(args: argparse.Namespace) -> Screen:
+    return read_csvs(
+        args.gRNA_counts_table_csv,
+        args.gRNA_info_table_csv,
+        args.samples_info_table_csv,
+        layers_filenames_dict={"edits": args.edits} if args.edits else None,
+    )