From bb240b9c2fea003d0e927820764b24fe4bef013e Mon Sep 17 00:00:00 2001
From: Remi Planel <rplanel@pasteur.fr>
Date: Wed, 29 Jan 2020 18:34:51 +0100
Subject: [PATCH] Can set seed size
---
crisprbact/predict.py | 6 ++++--
pyproject.toml | 2 +-
2 files changed, 5 insertions(+), 3 deletions(-)
diff --git a/crisprbact/predict.py b/crisprbact/predict.py
index 0c2cd5b..5b88c37 100644
--- a/crisprbact/predict.py
+++ b/crisprbact/predict.py
@@ -43,7 +43,7 @@ def find_targets(seq):
)
-def on_target_predict(seq, genome=None):
+def on_target_predict(seq, genome=None, seed_size=7):
seq = seq.upper() # make uppercase
seq = re.sub(r"\s", "", seq) # removes white space
@@ -63,11 +63,13 @@ def on_target_predict(seq, genome=None):
)
X = X.reshape(X.shape[0], -1)
preds = predict(X)
+
for i, target in enumerate(alltargets):
target.update({"pred": preds[i]})
+ target.update({"seed_size": seed_size})
if genome:
off_target_df = compute_off_target_df(
- target["guide"], 7, records, genome_features
+ target["guide"], seed_size, records, genome_features
)
off_target_list = []
features = off_target_df.loc[0:, "features"]
diff --git a/pyproject.toml b/pyproject.toml
index 627a66f..12da22e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
[tool.poetry]
name = "crisprbact"
-version = "0.2.0"
+version = "0.2.1"
license = "GPL-3.0"
description = "Tools to design and analyse CRISPRi experiments"
authors = ["David Bikard <david.bikard@pasteur.fr>", "Remi Planel <rplanel@pasteur.fr>"]
--
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