One entry per feature

crisprbact/cli.py

-from crisprbact.predict import on_target_predict
 from Bio import SeqIO
 import click
+from crisprbact.predict import on_target_predict
 
 
 class Config(object):

crisprbact/predict.py

@@ -71,16 +71,29 @@ def on_target_predict(seq, genome=None, seed_size=7):
                 off_target_df = compute_off_target_df(
                     target["guide"], seed_size, records, genome_features
                 )
-                off_target_list = []
-                features = off_target_df.loc[0:, "features"]
-                for feat in features:
-                    for x in feat:
-                        features_dict = {}
-                        for k, feat in x.qualifiers.items():
+                off_targets_list = []
+                off_targets = off_target_df.loc[
+                    0:, ["start", "end", "pampos", "features"]
+                ]
+                for index, off_t in enumerate(off_targets.values.tolist()):
+
+                    off_target_dict = {
+                        "off_target_start": off_t[0],
+                        "off_target_end": off_t[1],
+                        "pampos": off_t[2],
+                    }
+                    for feat in off_t[3]:
+                        feature_dict = {
+                            "feat_strand": feat.location.strand,
+                            "feat_start": feat.location.start,
+                            "feat_end": feat.location.end,
+                            "feat_type": feat.type,
+                        }
+                        for k, feat in feat.qualifiers.items():
                             if k != "translation":
-                                features_dict[k] = " :: ".join(feat)
-                        off_target_list.append(features_dict)
-                target.update({"off_targets": off_target_list})
+                                feature_dict[k] = " :: ".join(feat)
+                        off_targets_list.append({**feature_dict, **off_target_dict})
+                target.update({"off_targets": off_targets_list})
             else:
                 target.update({"off_targets": []})
         return alltargets

pyproject.toml

 [tool.poetry]
 name = "crisprbact"
-version = "0.2.1"
+version = "0.3.0"
 license = "GPL-3.0"
 description = "Tools to design and analyse CRISPRi experiments"
 authors = ["David Bikard <david.bikard@pasteur.fr>", "Remi Planel <rplanel@pasteur.fr>"]