Skip to content

Commit 5f19727

Browse files
committed
Fix renaming issue in vizgen loader
1 parent 02f6f55 commit 5f19727

File tree

1 file changed

+2
-0
lines changed
  • src/datasets/loaders/vizgen_merscope

1 file changed

+2
-0
lines changed

src/datasets/loaders/vizgen_merscope/script.py

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -201,8 +201,10 @@ def read_boundary_hdf5(folder):
201201
sdata["transcripts"] = sdata["transcripts"].rename(columns={"global_z": "z", "transcript_id": "ensembl_id"})#, "gene": "feature_name"})
202202
if "gene" in sdata["transcripts"].columns:
203203
# No idea why, but somehow dask dataframe renaming for the 'gene' column ends up in a key error when assigning it to sdata["transcripts"].
204+
# update: see https://github.com/scverse/spatialdata/issues/996
204205
sdata["transcripts"]["feature_name"] = sdata["transcripts"]["gene"]
205206
del sdata["transcripts"]["gene"]
207+
sdata['transcripts'].attrs["spatialdata_attrs"]["feature_key"] = "feature_name"
206208
print(datetime.now() - t0, "Renamed transcripts column 'global_z' -> 'z' and 'gene' -> 'feature_name' and 'transcript_id' -> 'ensembl_id'", flush=True)
207209

208210
print(datetime.now() - t0, "Columns in sdata['transcripts']:", sdata["transcripts"].columns, flush=True)

0 commit comments

Comments
 (0)