From c9f5cced51a8c3970b36003f32ec39e846af01d5 Mon Sep 17 00:00:00 2001
From: Remi Planel <rplanel@pasteur.fr>
Date: Tue, 17 Mar 2020 17:05:41 +0100
Subject: [PATCH] Add to the result the biggest match between the guide and the
off-target
---
crisprbact/predict.py | 17 ++++++++++++++---
1 file changed, 14 insertions(+), 3 deletions(-)
diff --git a/crisprbact/predict.py b/crisprbact/predict.py
index bb5c397..5609a91 100644
--- a/crisprbact/predict.py
+++ b/crisprbact/predict.py
@@ -89,7 +89,16 @@ def on_target_predict(seq, genome=None, seed_sizes=[8, 9, 10, 11, 12]):
if off_target_df is not None and not off_target_df.empty:
off_targets = off_target_df.loc[
0:,
- ["start", "end", "pampos", "strand", "recid", "features"],
+ [
+ "start",
+ "end",
+ "pampos",
+ "strand",
+ "recid",
+ "max_matching_len",
+ "max_matching_seq",
+ "features",
+ ],
]
for j, off_t in enumerate(off_targets.values.tolist()):
off_target_dict = {
@@ -103,12 +112,14 @@ def on_target_predict(seq, genome=None, seed_sizes=[8, 9, 10, 11, 12]):
"off_target_pampos": off_t[2],
"off_target_strand": off_t[3],
"off_target_recid": off_t[4],
+ "off_target_max_matching_seq": off_t[6],
"off_target_good_orientation": None,
}
+ index_features = 7
# Loop through features associated to an off-target position
- if len(off_t[5]) > 0:
+ if len(off_t[index_features]) > 0:
# Loop for each feature
- for feat in off_t[5]:
+ for feat in off_t[index_features]:
if get_strand_value(
off_target_dict["off_target_strand"]
) != get_strand_value(feat.location.strand):
--
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