From 5964446abdb41c064888edd996416d8cd3494fa1 Mon Sep 17 00:00:00 2001
From: Remi Planel <rplanel@pasteur.fr>
Date: Fri, 20 Mar 2020 12:00:50 +0100
Subject: [PATCH] Remove longest_perfect_match_length from dataframe
---
crisprbact/off_target.py | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/crisprbact/off_target.py b/crisprbact/off_target.py
index 886235f..89a5a64 100644
--- a/crisprbact/off_target.py
+++ b/crisprbact/off_target.py
@@ -47,8 +47,7 @@ def get_off_target_pos(guide, records, seed_size):
"pampos",
"strand",
"recid",
- "max_matching_len",
- "max_matching_seq",
+ "longest_perfect_match",
"pam_seq",
],
zip(*offs),
@@ -81,12 +80,12 @@ def gen_extract_off_target_strand_plus(
sub_sequence_to_match = sequence_string[start_pos_seq:end_pos_seq][::-1]
matching_chars = list(common_start(sub_sequence_to_match, guide_subseq))
matching_substr = "".join(matching_chars)
+ longest_perfect_match = matching_substr[::-1] + match.group(0)[:-3]
yield match.span() + (
match.end(),
"+",
seqid,
- seed_size + len(matching_chars),
- matching_substr[::-1] + match.group(0)[:-3],
+ longest_perfect_match,
match.group(0)[-3:],
)
@@ -114,12 +113,13 @@ def gen_extract_off_target_strand_minus(
guide_subseq = rev_comp(guide[: 20 - seed_size])
matching_chars = list(common_start(sub_sequence_to_match, guide_subseq))
matching_substr = "".join(matching_chars)
+ longest_perfect_match = match.group(0)[3:] + matching_substr
+
yield match.span() + (
match.start(),
"-",
seqid,
- seed_size + len(matching_chars),
- match.group(0)[3:] + matching_substr,
+ longest_perfect_match,
match.group(0)[:3],
)
--
GitLab