From aa7ca893c36777aa339c0d57d43e1a2666cc66ce Mon Sep 17 00:00:00 2001
From: Remi Planel <rplanel@pasteur.fr>
Date: Thu, 12 Mar 2020 16:50:00 +0100
Subject: [PATCH] Add todo
---
crisprbact/off_target.py | 3 +++
1 file changed, 3 insertions(+)
diff --git a/crisprbact/off_target.py b/crisprbact/off_target.py
index eb5ed88..39ffc9f 100644
--- a/crisprbact/off_target.py
+++ b/crisprbact/off_target.py
@@ -18,6 +18,7 @@ def get_off_target_pos(guide, recs, seed_size):
# + ori
offs_plus = re.finditer(guide[-seed_size:] + "[ATGC]GG", str(rec.seq))
offs = [match.span() + (match.end(), "+", rec.id) for match in offs_plus]
+ # TODO: comparer guide avec rec.seq[match.start():match.end()]
# - ori
offs_minus = re.finditer(
"CC[ATGC]" + rev_comp(guide[-seed_size:]), str(rec.seq)
@@ -25,6 +26,8 @@ def get_off_target_pos(guide, recs, seed_size):
offs += [
match.span() + (match.start(), "-", rec.id) for match in offs_minus
]
+ # comparer guide avec rec.seq[match.start():match.end()].reverse_complement()
+ # comparer les positions identique à partir de la fin et d'affilé.
offs_dict = dict(
zip(["start", "end", "pampos", "strand", "recid"], zip(*offs))
)
--
GitLab