From c88c9fed0d0ba96c10714efd6cf6ac44822d829d Mon Sep 17 00:00:00 2001
From: Remi Planel <rplanel@pasteur.fr>
Date: Thu, 30 Jan 2020 16:55:29 +0100
Subject: [PATCH] One entry per feature
---
crisprbact/cli.py | 2 +-
crisprbact/predict.py | 31 ++++++++++++++++++++++---------
pyproject.toml | 2 +-
3 files changed, 24 insertions(+), 11 deletions(-)
diff --git a/crisprbact/cli.py b/crisprbact/cli.py
index ffa0946..4eeaebd 100644
--- a/crisprbact/cli.py
+++ b/crisprbact/cli.py
@@ -1,6 +1,6 @@
-from crisprbact.predict import on_target_predict
from Bio import SeqIO
import click
+from crisprbact.predict import on_target_predict
class Config(object):
diff --git a/crisprbact/predict.py b/crisprbact/predict.py
index 5b88c37..265a7f0 100644
--- a/crisprbact/predict.py
+++ b/crisprbact/predict.py
@@ -71,16 +71,29 @@ def on_target_predict(seq, genome=None, seed_size=7):
off_target_df = compute_off_target_df(
target["guide"], seed_size, records, genome_features
)
- off_target_list = []
- features = off_target_df.loc[0:, "features"]
- for feat in features:
- for x in feat:
- features_dict = {}
- for k, feat in x.qualifiers.items():
+ off_targets_list = []
+ off_targets = off_target_df.loc[
+ 0:, ["start", "end", "pampos", "features"]
+ ]
+ for index, off_t in enumerate(off_targets.values.tolist()):
+
+ off_target_dict = {
+ "off_target_start": off_t[0],
+ "off_target_end": off_t[1],
+ "pampos": off_t[2],
+ }
+ for feat in off_t[3]:
+ feature_dict = {
+ "feat_strand": feat.location.strand,
+ "feat_start": feat.location.start,
+ "feat_end": feat.location.end,
+ "feat_type": feat.type,
+ }
+ for k, feat in feat.qualifiers.items():
if k != "translation":
- features_dict[k] = " :: ".join(feat)
- off_target_list.append(features_dict)
- target.update({"off_targets": off_target_list})
+ feature_dict[k] = " :: ".join(feat)
+ off_targets_list.append({**feature_dict, **off_target_dict})
+ target.update({"off_targets": off_targets_list})
else:
target.update({"off_targets": []})
return alltargets
diff --git a/pyproject.toml b/pyproject.toml
index 12da22e..7e03c6a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
[tool.poetry]
name = "crisprbact"
-version = "0.2.1"
+version = "0.3.0"
license = "GPL-3.0"
description = "Tools to design and analyse CRISPRi experiments"
authors = ["David Bikard <david.bikard@pasteur.fr>", "Remi Planel <rplanel@pasteur.fr>"]
--
GitLab