From 9b768d05c882f79279a09564eecc07bf217debde Mon Sep 17 00:00:00 2001
From: Remi Planel <rplanel@pasteur.fr>
Date: Wed, 18 Mar 2020 14:57:00 +0100
Subject: [PATCH] Add the off-target PAM seq
---
crisprbact/predict.py | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/crisprbact/predict.py b/crisprbact/predict.py
index 5609a91..90bd810 100644
--- a/crisprbact/predict.py
+++ b/crisprbact/predict.py
@@ -31,10 +31,11 @@ def find_targets(seq):
seq_revcomp = rev_comp(seq)
matching_target = re.finditer("(?=([ATGC]{6}" + repam + "[ATGC]{16}))", seq_revcomp)
for target in matching_target:
+ matching_target = target.group(1)
yield dict(
[
- ("target", target.group(1)),
- ("guide", target.group(1)[:20]),
+ ("target", matching_target),
+ ("guide", matching_target[:20]),
("start", L - target.start() - 20),
("stop", L - target.start()),
("pam", L - target.start() - 22),
@@ -97,6 +98,7 @@ def on_target_predict(seq, genome=None, seed_sizes=[8, 9, 10, 11, 12]):
"recid",
"max_matching_len",
"max_matching_seq",
+ "pam_seq",
"features",
],
]
@@ -113,9 +115,10 @@ def on_target_predict(seq, genome=None, seed_sizes=[8, 9, 10, 11, 12]):
"off_target_strand": off_t[3],
"off_target_recid": off_t[4],
"off_target_max_matching_seq": off_t[6],
+ "off_target_pam_seq": off_t[7],
"off_target_good_orientation": None,
}
- index_features = 7
+ index_features = 8
# Loop through features associated to an off-target position
if len(off_t[index_features]) > 0:
# Loop for each feature
@@ -145,8 +148,6 @@ def on_target_predict(seq, genome=None, seed_sizes=[8, 9, 10, 11, 12]):
off_targets_list.append(
{**feature_dict, **off_target_dict}
)
- # elif not has_feature:
- # off_targets_list.append(off_target_dict)
else:
off_targets_list.append(off_target_dict)
off_targets_per_seed.append(
@@ -164,7 +165,6 @@ def on_target_predict(seq, genome=None, seed_sizes=[8, 9, 10, 11, 12]):
"off_targets": [],
}
)
- # target.update({"off_targets": off_targets_list})
target.update({"off_targets_per_seed": off_targets_per_seed})
else:
target.update({"off_targets_per_seed": []})
--
GitLab