From 726c47cd0d7a0ca779e28299ccdbab8eb4386238 Mon Sep 17 00:00:00 2001
From: Remi Planel <rplanel@pasteur.fr>
Date: Wed, 29 Jan 2020 16:29:43 +0100
Subject: [PATCH] features qualifiers in object
---
crisprbact/cli.py | 1 +
crisprbact/predict.py | 6 +++---
2 files changed, 4 insertions(+), 3 deletions(-)
diff --git a/crisprbact/cli.py b/crisprbact/cli.py
index 594206b..ffa0946 100644
--- a/crisprbact/cli.py
+++ b/crisprbact/cli.py
@@ -76,6 +76,7 @@ def from_seq(config, target, seq_format, output_file): # genome,
for record in SeqIO.parse(target, seq_format):
if config.verbose:
click.secho(" - search guide RNAs for %s " % record.id, fg=fg)
+ # g = SeqIO.parse(genome, "genbank")
guide_rnas = on_target_predict(str(record.seq))
write_guide_rnas(guide_rnas, output_file, record.id)
diff --git a/crisprbact/predict.py b/crisprbact/predict.py
index a34429a..0c2cd5b 100644
--- a/crisprbact/predict.py
+++ b/crisprbact/predict.py
@@ -72,12 +72,12 @@ def on_target_predict(seq, genome=None):
off_target_list = []
features = off_target_df.loc[0:, "features"]
for feat in features:
- features_list = []
for x in feat:
+ features_dict = {}
for k, feat in x.qualifiers.items():
if k != "translation":
- features_list.append((k, feat))
- off_target_list.append(features_list)
+ features_dict[k] = " :: ".join(feat)
+ off_target_list.append(features_dict)
target.update({"off_targets": off_target_list})
else:
target.update({"off_targets": []})
--
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