From f03c3f3026792d5f5146e56b99a732196a2b6ee1 Mon Sep 17 00:00:00 2001
From: Remi Planel <rplanel@pasteur.fr>
Date: Fri, 3 Apr 2020 12:08:18 +0200
Subject: [PATCH] Fix bug on guide sequence #10
---
crisprbact/predict.py | 39 ++++++++++++++++++++++++++-------------
1 file changed, 26 insertions(+), 13 deletions(-)
diff --git a/crisprbact/predict.py b/crisprbact/predict.py
index 49ed322..d4dc6a5 100644
--- a/crisprbact/predict.py
+++ b/crisprbact/predict.py
@@ -29,19 +29,32 @@ def find_targets(seq):
repam = "[ATGC]GG"
L = len(seq)
seq_revcomp = rev_comp(seq)
- matching_target = re.finditer("(?=([ATGC]{6}" + repam + "[ATGC]{16}))", seq_revcomp)
- for target in matching_target:
+ matching_targets = re.finditer(
+ "(?=([ATGC]{6}" + repam + "[ATGC]{16}))", seq_revcomp
+ )
+ for target in matching_targets:
matching_target = target.group(1)
- yield dict(
- [
- ("target", matching_target),
- ("guide", matching_target[:20]),
- ("start", L - target.start() - 20),
- ("stop", L - target.start()),
- ("pam", L - target.start() - 22),
- ("ori", "-"),
- ]
- )
+ start, end = target.span(1)
+ start_min = 13
+ if start >= start_min:
+ guide_start = start - start_min
+ guide_end = start + 7
+ guide = seq_revcomp[guide_start:guide_end]
+ assert len(guide) == 20
+ pos_seq_start = L - guide_start - 20
+ pos_seq_stop = L - guide_start
+ pos_seq_pam = pos_seq_start - 3
+ yield dict(
+ [
+ ("target", matching_target),
+ # ("guide", matching_target[:20]),
+ ("guide", guide),
+ ("start", pos_seq_start),
+ ("stop", pos_seq_stop),
+ ("pam", pos_seq_pam),
+ ("ori", "-"),
+ ]
+ )
def get_strand_value(value):
@@ -63,7 +76,7 @@ def on_target_predict(seq, genome=None, seed_sizes=[8, 9, 10, 11, 12]):
)
else:
genome_features = extract_features(records)
-
+ print(seq)
alltargets = list(find_targets(seq))
if alltargets:
X = np.array(
--
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