From b9ee273f554e773d640ef961ee65619fa62a8250 Mon Sep 17 00:00:00 2001
From: Remi Planel <rplanel@pasteur.fr>
Date: Fri, 31 Jan 2020 16:07:13 +0100
Subject: [PATCH] Fix bug no off-target feature. Fix #6
---
CHANGELOG | 4 ++++
crisprbact/predict.py | 55 ++++++++++++++++++++++++-------------------
2 files changed, 35 insertions(+), 24 deletions(-)
diff --git a/CHANGELOG b/CHANGELOG
index 6328333..9e5c7de 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,3 +1,7 @@
+# 0.3.2
+- Fix bugg when no off-target feature
+- Handle genome in fasta file
+
# 0.3.1
- Fix bug when no feature
- Add off-target strand to output
diff --git a/crisprbact/predict.py b/crisprbact/predict.py
index 14a3eac..20e97dd 100644
--- a/crisprbact/predict.py
+++ b/crisprbact/predict.py
@@ -72,31 +72,38 @@ def on_target_predict(seq, genome=None, seed_size=7):
target["guide"], seed_size, records, genome_features
)
off_targets_list = []
- off_targets = off_target_df.loc[
- 0:, ["start", "end", "pampos", "strand", "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],
- "strand": off_t[3],
- }
- if len(off_t[4]) > 0:
- for feat in off_t[4]:
- 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":
- feature_dict[k] = " :: ".join(feat)
+ if not off_target_df.empty:
+ off_targets = off_target_df.loc[
+ 0:, ["start", "end", "pampos", "strand", "recid", "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],
+ "strand": off_t[3],
+ "recid": off_t[4],
+ }
+ if len(off_t[5]) > 0:
+ # Loop for each feature
+ for feat in off_t[5]:
+ 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":
+ feature_dict[k] = "::".join(feat)
+ off_targets_list.append(
+ {**feature_dict, **off_target_dict}
+ )
+ else:
off_targets_list.append(off_target_dict)
- else:
- off_targets_list.append({**feature_dict, **off_target_dict})
- target.update({"off_targets": off_targets_list})
+ target.update({"off_targets": off_targets_list})
+ else:
+ target.update({"off_targets": off_targets_list})
else:
target.update({"off_targets": []})
return alltargets
--
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