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[MRG] Adding picklist arg to sourmash_args.load_picklist to allow the option #3839

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[MRG] Adding picklist arg to sourmash_args.load_picklist to allow the option #3839

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5ad017d
adding picklist arg to load_picklist to remove the entire namespace f…
ccbaumler Oct 23, 2025
ecdbc56
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Oct 23, 2025
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25 changes: 15 additions & 10 deletions src/sourmash/sourmash_args.py
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Original file line number Diff line number Diff line change
Expand Up @@ -124,34 +124,39 @@ def calculate_moltype(args, default=None):
return moltype


def load_picklist(args):
def load_picklist(args=None, picklist=None):
"Load a SignaturePicklist from --picklist arguments."
picklist = None
if args.picklist:
if args is None:
picklist = picklist
elif isinstance(args, (str, bytes)):
picklist = args

picklist_obj = None
if picklist:
try:
picklist = SignaturePicklist.from_picklist_args(args.picklist)
picklist_obj = SignaturePicklist.from_picklist_args(picklist)

notify(
f"picking column '{picklist.column_name}' of type '{picklist.coltype}' from '{picklist.pickfile}'"
f"picking column '{picklist_obj.column_name}' of type '{picklist_obj.coltype}' from '{picklist_obj.pickfile}'"
)

n_empty_val, dup_vals = picklist.load()
n_empty_val, dup_vals = picklist_obj.load()
except ValueError as exc:
error("ERROR: could not load picklist.")
error(str(exc))
sys.exit(-1)

notify(f"loaded {len(picklist.pickset)} distinct values into picklist.")
notify(f"loaded {len(picklist_obj.pickset)} distinct values into picklist.")
if n_empty_val:
notify(
f"WARNING: {n_empty_val} empty values in column '{picklist.column_name}' in picklist file"
f"WARNING: {n_empty_val} empty values in column '{picklist_obj.column_name}' in picklist file"
)
if dup_vals:
notify(
f"WARNING: {len(dup_vals)} values in picklist column '{picklist.column_name}' were not distinct"
f"WARNING: {len(dup_vals)} values in picklist column '{picklist_obj.column_name}' were not distinct"
)

return picklist
return picklist_obj


def report_picklist(args, picklist):
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