diff --git a/crisprbact/cli.py b/crisprbact/cli.py
index 9568ddddf5980ad73bb864e2dd5a1ddfc9b549db..390fc8f202aabe0a1c2dcf5841fe8d6b43bc2931 100644
--- a/crisprbact/cli.py
+++ b/crisprbact/cli.py
@@ -94,7 +94,7 @@ def from_str(
guide_rnas = on_target_predict(target, genome_fh)
click.echo("\t".join(HEADER), file=output_file)
- write_guide_rnas(guide_rnas, output_file)
+ write_guide_rnas(guide_rnas, output_file, len(HEADER))
@predict.command()
@@ -150,6 +150,7 @@ def from_seq(
fg = "blue"
if config.verbose:
print_parameters(target.name, fg)
+
click.echo("\t".join(HEADER), file=output_file)
for record in SeqIO.parse(target, seq_format):
if config.verbose:
@@ -160,7 +161,7 @@ def from_seq(
genome_fh = None
guide_rnas = on_target_predict(str(record.seq), genome_fh)
# print(guide_rnas)
- write_guide_rnas(guide_rnas, output_file, record.id)
+ write_guide_rnas(guide_rnas, output_file, len(HEADER), record.id)
def print_parameters(target, fg="blue"):
@@ -168,7 +169,9 @@ def print_parameters(target, fg="blue"):
click.secho("Target sequence : %s" % target, fg=fg)
-def write_guide_rnas(guide_rnas, output_file, seq_id="N/A"):
+def write_guide_rnas(
+ guide_rnas, output_file, header_size, seq_id="N/A",
+):
for guide_rna in guide_rnas:
row = [
str(guide_rna["target_id"]),
@@ -179,6 +182,7 @@ def write_guide_rnas(guide_rnas, output_file, seq_id="N/A"):
str(guide_rna["pred"]),
seq_id,
]
+ # seed_size = ""
if len(guide_rna["off_targets_per_seed"]) > 0:
for off_target_per_seed in guide_rna["off_targets_per_seed"]:
for off_target in off_target_per_seed["off_targets"]:
@@ -191,14 +195,16 @@ def write_guide_rnas(guide_rnas, output_file, seq_id="N/A"):
return ""
details = map(extract_off_target_detail, OFF_TARGET_DETAILS)
+ line_to_print = row + [str(seed_size)] + list(details)
+ assert len(line_to_print) == header_size
click.echo(
- "\t".join(row + [str(seed_size)] + list(details)),
- file=output_file,
+ "\t".join(line_to_print), file=output_file,
)
else:
+ line_to_print = row + [""] + list(map(lambda x: "", OFF_TARGET_DETAILS))
+ assert len(line_to_print) == header_size
click.echo(
- "\t".join(row + list(map(lambda x: "", OFF_TARGET_DETAILS))),
- file=output_file,
+ "\t".join(line_to_print), file=output_file,
)
diff --git a/crisprbact/predict.py b/crisprbact/predict.py
index 3a10c6f7e6a40fe73b8a9b31032b1bda7d4c7d7f..41d1579ce5d19cd37d27b8bae304c2467ae05971 100644
--- a/crisprbact/predict.py
+++ b/crisprbact/predict.py
@@ -68,6 +68,7 @@ def on_target_predict(seq, genome=None, seed_sizes=[8, 9, 10, 11, 12, GUIDE_LEN]
seq = re.sub(r"\s", "", seq) # removes white space
records = None
genome_features = None
+
if genome:
records = extract_records(genome)
if records is None:
@@ -87,69 +88,11 @@ def on_target_predict(seq, genome=None, seed_sizes=[8, 9, 10, 11, 12, GUIDE_LEN]
target.update({"target_id": target_id})
target.update({"pred": preds[i]})
if genome:
- off_targets_per_seed = []
- for seed_size in seed_sizes:
- # off-target found for a guide
- off_target_df = compute_off_target_df(
- target["guide"], seed_size, records, genome_features
- )
- off_targets_list = []
- if off_target_df is not None and not off_target_df.empty:
- off_targets = slice_off_targets_results(off_target_df)
- for j, off_t in enumerate(off_targets):
- off_target_dict = {
- "off_target_id": str(target_id)
- + "-"
- + str(seed_size)
- + "-"
- + str(j),
- "off_target_start": off_t[0],
- "off_target_end": off_t[1],
- "off_target_pampos": off_t[2],
- "off_target_strand": off_t[3],
- "off_target_recid": off_t[4],
- "off_target_longest_perfect_match": off_t[5],
- "off_target_pam_seq": off_t[6],
- "off_target_good_orientation": None,
- }
- if (
- seed_size == GUIDE_LEN
- or off_target_dict["off_target_longest_perfect_match"]
- != GUIDE_LEN
- ):
- index_features = 7
- # Get feature details associated
- # to an off-target position
- if len(off_t[index_features]) > 0:
- feat = off_t[index_features][0]
- off_target_dict[
- "off_target_good_orientation"
- ] = is_good_orientation(
- feat, off_target_dict["off_target_strand"]
- )
- off_target_feature = get_off_target_feature(feat)
- off_targets_list.append(
- {**off_target_feature, **off_target_dict}
- )
- else:
- off_targets_list.append(off_target_dict)
-
- off_targets_per_seed.append(
- {
- "id": str(i) + "-" + str(seed_size),
- "seed_size": seed_size,
- "off_targets": off_targets_list,
- }
- )
- else:
- off_targets_per_seed.append(
- {
- "id": str(i) + "-" + str(seed_size),
- "seed_size": seed_size,
- "off_targets": [],
- }
- )
- target.update({"off_targets_per_seed": off_targets_per_seed})
+ # lookup for off-targets in genome
+ off_targets_per_seed = gen_off_target_per_seed_size(
+ i, target["guide"], records, genome_features, target_id, seed_sizes
+ )
+ target.update({"off_targets_per_seed": list(off_targets_per_seed)})
else:
target.update({"off_targets_per_seed": []})
return alltargets
@@ -204,4 +147,58 @@ def get_off_target_feature(feat):
return feature_dict
-# def gen_off_target_per_seed_size(seed_sizes):
+def gen_off_target_per_seed_size(
+ index, guide, records, genome_features, target_id, seed_sizes
+):
+ for seed_size in seed_sizes:
+ # off-target found for a guide
+ off_target_df = compute_off_target_df(
+ guide, seed_size, records, genome_features
+ )
+ if off_target_df is not None and not off_target_df.empty:
+ off_targets = slice_off_targets_results(off_target_df)
+ off_targets_list = gen_off_targets_convert(
+ target_id, seed_size, off_targets
+ )
+ yield {
+ "id": str(index) + "-" + str(seed_size),
+ "seed_size": seed_size,
+ "off_targets": off_targets_list,
+ }
+ else:
+ yield {
+ "id": str(index) + "-" + str(seed_size),
+ "seed_size": seed_size,
+ "off_targets": [],
+ }
+
+
+def gen_off_targets_convert(target_id, seed_size, off_targets):
+ for j, off_t in enumerate(off_targets):
+ off_target_dict = {
+ "off_target_id": str(target_id) + "-" + str(seed_size) + "-" + str(j),
+ "off_target_start": off_t[0],
+ "off_target_end": off_t[1],
+ "off_target_pampos": off_t[2],
+ "off_target_strand": off_t[3],
+ "off_target_recid": off_t[4],
+ "off_target_longest_perfect_match": off_t[5],
+ "off_target_pam_seq": off_t[6],
+ "off_target_good_orientation": None,
+ }
+ if (
+ seed_size == GUIDE_LEN
+ or off_target_dict["off_target_longest_perfect_match"] != GUIDE_LEN
+ ):
+ index_features = 7
+ # Get feature details associated
+ # to an off-target position
+ if len(off_t[index_features]) > 0:
+ feat = off_t[index_features][0]
+ off_target_dict["off_target_good_orientation"] = is_good_orientation(
+ feat, off_target_dict["off_target_strand"]
+ )
+ off_target_feature = get_off_target_feature(feat)
+ yield {**off_target_feature, **off_target_dict}
+ else:
+ yield off_target_dict