add missing file

bean/plotting/parser.py

@@ -0,0 +1,52 @@
+import argparse
+
+def parse_args(parser=None):
+    if parser is None:
+        parser = argparse.ArgumentParser()
+    parser.add_argument(
+        "bdata_path", help="Path to the ReporterScreen object to run QC on", type=str
+    )
+    parser.add_argument(
+        "-o",
+        "--output-prefix",
+        help="Output prefix of editing pattern report (prefix.html, prefix.ipynb). If not provided, base name of `bdata_path` is used.",
+        type=str,
+    )
+    parser.add_argument(
+        "--replicate-col",
+        help="Column name in `bdata.samples` that describes replicate ID.",
+        type=str,
+        default="replicate",
+    )
+    parser.add_argument(
+        "--condition-col",
+        help="Column name in `bdata.samples` that describes experimental condition. (sorting bin, time, etc.)",
+        type=str,
+        default="condition",
+    )
+    parser.add_argument(
+        "--pam-col",
+        help="Column name describing PAM of each gRNA in `bdata.guides`.",
+        type=str,
+        default=None,
+    )
+    parser.add_argument(
+        "--control-condition",
+        help="Control condition where editing preference would be profiled at. Pre-filters data where `bdata.samples[condition_col] == control_condition`.",
+        type=str,
+        default="bulk",
+    )
+    parser.add_argument(
+        "-w",
+        "--window-length",
+        help="Window length of editing window of maximal editing efficiency to be identified. This window is used to quantify context specificity within the window.",
+        type=int,
+        default=6,
+    )
+    parser.add_argument(
+        "--save-fig",
+        action="store_true",
+        help="Save .pdf of the figures included in the report.",
+    )
+
+    return parser