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Hotfix/query cli #209

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merged 3 commits into from
Nov 19, 2024
Merged

Hotfix/query cli #209

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5e5fc0a
cluster cli compatibility for in-/exclude class/category
nlouwen Nov 18, 2024
a098509
update logging warnings
nlouwen Nov 18, 2024
c709ddd
update logging
nlouwen Nov 19, 2024
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4 changes: 4 additions & 0 deletions big_scape/cli/query_cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -91,6 +91,10 @@ def query(ctx, *args, **kwarg):
ctx.obj["mix"] = None
ctx.obj["hybrids_off"] = False
ctx.obj["mode"] = "Query"
ctx.obj["exclude_categories"] = None
ctx.obj["include_categories"] = None
ctx.obj["exclude_classes"] = None
ctx.obj["include_classes"] = None

# workflow validations
validate_pfam_path(ctx)
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2 changes: 1 addition & 1 deletion big_scape/file_input/load_files.py
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Expand Up @@ -197,7 +197,7 @@ def remove_duplicate_gbk(gbks: list[GBK]) -> list[GBK]:
unique_gbks = set()
for gbk in gbks:
if gbk in unique_gbks:
logging.info("Skipping duplicate %s", gbk)
logging.info("Skipping duplicate %s", gbk.path)
continue
unique_gbks.add(gbk)

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22 changes: 22 additions & 0 deletions big_scape/genbank/bgc_record.py
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Expand Up @@ -403,13 +403,20 @@ def get_sub_records(
Returns:
list[BGCRecord]: list of records of the specified type
"""
err_path = region.parent_gbk.path if region.parent_gbk else ""

if region is None:
return []

if record_type == bs_enums.genbank.RECORD_TYPE.REGION:
return [region]

if region.cand_clusters is None:
logging.warning(
"%s: No %s records found, using region instead.",
err_path,
record_type.value,
)
return [region]

cand_clusters = [
Expand All @@ -419,6 +426,11 @@ def get_sub_records(
]

if len(cand_clusters) == 0:
logging.warning(
"%s: No %s records found, using region instead.",
err_path,
record_type.value,
)
return [region]

# TODO: check if properly implemented, or at all
Expand All @@ -445,6 +457,11 @@ def get_sub_records(
proto_cluster_numbers.append(proto_cluster.number)

if len(proto_clusters) == 0:
logging.warning(
"%s: No %s records found, using cand_cluster instead.",
err_path,
record_type.value,
)
return cand_clusters

if record_type == bs_enums.genbank.RECORD_TYPE.PROTO_CLUSTER:
Expand All @@ -461,6 +478,11 @@ def get_sub_records(
proto_core_numbers.append(proto_core.number)

if len(proto_cores) == 0:
logging.warning(
"%s: No %s records found, using protocluster instead.",
err_path,
record_type.value,
)
return proto_clusters

return proto_cores
2 changes: 1 addition & 1 deletion big_scape/run_bigscape.py
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Expand Up @@ -272,7 +272,7 @@ def signal_handler(sig, frame):
pfam_info = HMMer.get_pfam_info()
HMMer.unload()

logging.info("Generating GCF alignments, trees and outputfiles")
logging.info("Generating GCF trees and output files")

# prepare output files
legacy_prepare_output(run["output_dir"], pfam_info)
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