changed how sc_ref is copied in

Habib Rehman · Habib Rehman · commit 6a2183e65f11 · 2024-11-13T09:15:03.000-05:00
diff --git a/src/methods_transcript_assignment/pciSeq_transcript_assignment/script.py b/src/methods_transcript_assignment/pciSeq_transcript_assignment/script.py
@@ -91,6 +91,8 @@
 # print(opts)
 
 input_scrnaseq = ad.read_h5ad(par['input_scrnaseq'])
+input_scrnaseq.X = input_scrnaseq.layers['counts']
+
 assignments, cell_types = tx.preprocessing.run_pciSeq(
     transcripts_dataframe,
     label_image,
