features-barcodes-only

[joshua-gould]

No description provided.

[jshleap]

Suggested change

	query_columns = [
	c
	for c in query_columns
	if c not in merged_df.columns and c in data.var.index
	]
	columns.update(query_columns)
	columns.update(
	c for c in query_columns
	if c not in merged_df.columns and c in data.var.index
	)

[jshleap]

Suggested change

	for i in range(len(columns)):
	merged_df[columns[i]] = values[:, i]
	if sp.issparse(values):
	values = values.toarray()
	merged_df[columns] = values

[jshleap]

if we need to test for sparcity (I think is a failsafe) we need to import scipy.sparse as sp

[jshleap]

Is intended that --objects and --merge can be used?

[jshleap]

Suggested change

	for i in range(len(phenotype_paths)):
	# match */A1-*.parquet and */A1.parquet
	sep = phenotype_filesystems[i].sep
	matches = phenotype_filesystems[i].glob(
	f"{phenotype_paths[i]}{sep}*{sep}{image_key}-*.parquet"
	) + phenotype_filesystems[i].glob(
	f"{phenotype_paths[i]}{sep}*{sep}{image_key}.parquet"
	)
	if len(matches) == 0:
	# match A1-*.parquet and A1.parquet
	matches = phenotype_filesystems[i].glob(
	f"{phenotype_paths[i]}{sep}{image_key}-*.parquet"
	) + phenotype_filesystems[i].glob(
	f"{phenotype_paths[i]}{sep}{image_key}.parquet"
	)
	for x in matches:
	_phenotype_paths.append(phenotype_filesystems[i].unstrip_protocol(x))
	if phenotype_suffix is not None:
	_phenotype_suffix.append(phenotype_suffix[i])
	return _phenotype_paths, _phenotype_suffix
	has_suffix = phenotype_suffix is not None
	suffix_iter = phenotype_suffix if has_suffix else [None] * len(phenotype_paths)
	for path, fs, suffix in zip(phenotype_paths, phenotype_filesystems, suffix_iter, strict=True):
	sep = fs.sep
	# Match */<image_key>[-*].parquet (subdirectory pattern)
	matches = (
	fs.glob(f"{path}{sep}*{sep}{image_key}-*.parquet")
	+ fs.glob(f"{path}{sep}*{sep}{image_key}.parquet")
	)
	if not matches:
	# Match <image_key>[-*].parquet (flat pattern)
	matches = (
	fs.glob(f"{path}{sep}{image_key}-*.parquet")
	+ fs.glob(f"{path}{sep}{image_key}.parquet")
	)
	for match in matches:
	phenotypepaths.append(fs.unstrip_protocol(match))
	if has_suffix:
	phenotypesuffix.append(suffix)
	return phenotypepaths, phenotypesuffix