From 5e30c299509011d09360084a564aa54f355a9b81 Mon Sep 17 00:00:00 2001
From: jalil <jalil.nourisa@gmail.com>
Date: Wed, 21 Aug 2024 21:20:53 +0200
Subject: [PATCH] granie bug fixed

---
 src/methods/multi_omics/granie/script.R | 4 ++--
 src/metrics/regression_1/main.py        | 7 +++----
 src/metrics/regression_2/main.py        | 3 ++-
 3 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/methods/multi_omics/granie/script.R b/src/methods/multi_omics/granie/script.R
index 752e1b0c4..a41cd9918 100644
--- a/src/methods/multi_omics/granie/script.R
+++ b/src/methods/multi_omics/granie/script.R
@@ -101,12 +101,12 @@ if (!file.exists(file_RNA)) {
 if (par$forceRerun | !file.exists(file_seurat)) {
   
  # Sparse matrix
- rna.m = readRDS(par$perturbation_rna)
+ rna.m = readRDS(par$multiomics_rna)
  
  seurat_object <- CreateSeuratObject(count = rna.m, project = "PBMC", min.cells = 1, min.features = 1, assay = "RNA")
  
  # RangedSummarizedExperiment
- atac = readRDS(par$perturbation_atac)
+ atac = readRDS(par$multiomics_atac)
  
  # Extract counts and metadata from the RangedSummarizedExperiment
   atac_counts <- assays(atac)$counts
diff --git a/src/metrics/regression_1/main.py b/src/metrics/regression_1/main.py
index 6a2149f16..2e5d4dbc4 100644
--- a/src/metrics/regression_1/main.py
+++ b/src/metrics/regression_1/main.py
@@ -65,9 +65,6 @@ def regression_1(
     """
     gene_names = train_df.index.to_numpy()
     gene_names_grn = net.index.to_numpy()
-    print(net)
-    print(gene_names)
-    aa
     # determine regressor 
     if reg_type=='ridge':
         regr =  Ridge(**dict(random_state=32))
@@ -175,8 +172,10 @@ def main(par):
     print('Reading input files', flush=True)
     
     perturbation_data = ad.read_h5ad(par['perturbation_data'])
+    # perturbation_data = perturbation_data[:, :2000]
+    # print(perturbation_data)
     gene_names = perturbation_data.var.index.to_numpy()
-    net = pd.read_csv(par['prediction'], index_col=0)
+    net = pd.read_csv(par['prediction'])
 
     subsample = par['subsample']
     reg_type = par['reg_type']
diff --git a/src/metrics/regression_2/main.py b/src/metrics/regression_2/main.py
index 2707cfb33..cc3dc3d58 100644
--- a/src/metrics/regression_2/main.py
+++ b/src/metrics/regression_2/main.py
@@ -231,10 +231,11 @@ def main(par: Dict[str, Any]) -> pd.DataFrame:
     gene_names = perturbation_data.var.index.to_numpy()
     n_genes = len(gene_names)
     groups = LabelEncoder().fit_transform(perturbation_data.obs.plate_name)
+
     
     # Load inferred GRN
     print(f'Loading GRN', flush=True)
-    grn = load_grn(par['prediction'], gene_names)
+    grn = pd.read_csv(par['prediction'])
     
     # Load and standardize perturbation data
     layer = par['layer']