save reporter structure during counting

pinellolab · May 7, 2024 · c9c1194 · c9c1194
1 parent 204fb66
commit c9c1194
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Showing 5 changed files with 28 additions and 4 deletions.
diff --git a/bean/annotate/utils.py b/bean/annotate/utils.py
@@ -297,13 +297,13 @@ def parse_args(parser=None):
     parser.add_argument(
         "--reporter-length",
         type=int,
-        default=32,
+        default=None,
         help="Length of reporter sequence in the construct.",
     )
     parser.add_argument(
         "--reporter-right-flank-length",
         type=int,
-        default=6,
+        default=None,
         help="Length of the right-flanking nucleotides of protospacer in the reporter.",
     )
     parser.add_argument(

diff --git a/bean/cli/filter.py b/bean/cli/filter.py
@@ -43,6 +43,18 @@ def main(args):
     args = check_args(args)
     if not args.load_tmp:
         bdata = be.read_h5ad(args.bdata_path)
+        if args.reporter_length is None:
+            if "reporter_length" in bdata.uns:
+                args.reporter_length = bdata.uns["reporter_length"]
+            else:
+                args.reporter_length = 32
+        if args.reporter_right_flank_length is None:
+            if "reporter_right_flank_length" in bdata.uns:
+                args.reporter_right_flank_length = bdata.uns[
+                    "reporter_right_flank_length"
+                ]
+            else:
+                args.reporter_right_flank_length = 6
         allele_df_keys = ["allele_counts"]
         info(
             f"Starting from .uns['allele_counts'] with {len(bdata.uns['allele_counts'])} alleles."

diff --git a/bean/mapping/GuideEditCounter.py b/bean/mapping/GuideEditCounter.py
@@ -112,6 +112,8 @@ def __init__(self, **kwargs):
             tiling=kwargs["tiling"],
         )
         self.screen.guides["guide_len"] = self.screen.guides.sequence.map(len)
+        self.screen.uns["reporter_length"] = kwargs["reporter_length"]
+        self.screen.uns["reporter_right_flank_length"] = kwargs["reporter_length"] - kwargs["gstart_reporter"] - self.screen.guides["guide_len"].max()
         self.count_guide_edits = kwargs["count_guide_edits"]
         if self.count_guide_edits:
             self.screen.uns["guide_edit_counts"] = {}

diff --git a/bean/qc/parser.py b/bean/qc/parser.py
@@ -154,13 +154,13 @@ def parse_args(parser=None):
     parser.add_argument(
         "--reporter-length",
         type=int,
-        default=32,
+        default=None,
         help="Length of reporter sequence in the construct.",
     )
     parser.add_argument(
         "--reporter-right-flank-length",
         type=int,
-        default=6,
+        default=None,
         help="Length of the right-flanking nucleotides of protospacer in the reporter.",
     )
     return parser
diff --git a/bean/qc/utils.py b/bean/qc/utils.py
@@ -61,6 +61,16 @@ def check_args(args):
         args.base_edit_data = False
     else:
         args.base_edit_data = True
+    if args.reporter_length is None:
+        if "reporter_length" in bdata.uns:
+            args.reporter_length = bdata.uns["reporter_length"]
+        else:
+            args.reporter_length = 32
+    if args.reporter_right_flank_length is None:
+        if "reporter_right_flank_length" in bdata.uns:
+            args.reporter_right_flank_length = bdata.uns["reporter_right_flank_length"]
+        else:
+            args.reporter_right_flank_length = 6
     return args