fix downloaded file paths

app.py

@@ -15,23 +15,6 @@ from itertools import chain
 from huggingface_hub import hf_hub_download
 
 
-def unzip(file):
-    with gzip.open(file, 'rb') as f_in:
-        with open(file.replace('.gz', ''), 'wb') as f_out:
-            shutil.copyfileobj(f_in, f_out)
-
-
-hf_hub_download(repo_id="dylanplummer/islet-epigenome", filename="rna.h5ad.gz", repo_type="dataset", token=os.environ['DATASET_SECRET'])
-hf_hub_download(repo_id="dylanplummer/islet-epigenome", filename="hic.h5ad.gz", repo_type="dataset", token=os.environ['DATASET_SECRET'])
-hf_hub_download(repo_id="dylanplummer/islet-epigenome", filename="dcq_prior_10kb_ice_0.99.graphml.gz", repo_type="dataset", token=os.environ['DATASET_SECRET'])
-unzip('rna.h5ad.gz')
-unzip('hic.h5ad.gz')
-
-hf_hub_download(repo_id="dylanplummer/HiGLUE-islet", filename="glue_hic_dcq_prior_10kb_ice_0.99.dill", repo_type="model", token=os.environ['DATASET_SECRET'])
-
-
-
-
 prior_name = 'dcq'
 resolution = '10kb'
 loop_q = 0.99
@@ -43,7 +26,28 @@ window_size = 64
 eps = 1e-4
 n_neighbors = 5
 
-rna = ad.read_h5ad(f"rna.h5ad")
+
+def unzip(file):
+    with gzip.open(file, 'rb') as f_in:
+        new_file = file.replace('.gz', '')
+        with open(new_file, 'wb') as f_out:
+            shutil.copyfileobj(f_in, f_out)
+    return new_file
+
+
+rna_file = hf_hub_download(repo_id="dylanplummer/islet-epigenome", filename="rna.h5ad.gz", repo_type="dataset", token=os.environ['DATASET_SECRET'])
+hic_file = hf_hub_download(repo_id="dylanplummer/islet-epigenome", filename="hic.h5ad.gz", repo_type="dataset", token=os.environ['DATASET_SECRET'])
+graph_file = hf_hub_download(repo_id="dylanplummer/islet-epigenome", filename=f"{prior_name}_prior_{resolution}_{suffix}.graphml.gz", repo_type="dataset", token=os.environ['DATASET_SECRET'])
+rna_file = unzip(rna_file)
+hic_file = unzip('hic.h5ad.gz')
+
+model_file = hf_hub_download(repo_id="dylanplummer/HiGLUE-islet", filename=f"glue_hic_{prior_name}_prior_{resolution}_{suffix}.dill", repo_type="model", token=os.environ['DATASET_SECRET'])
+
+
+
+
+
+rna = ad.read_h5ad(rna_file)
 scglue.models.configure_dataset(rna, "NB", use_highly_variable=True, use_rep="X_pca", use_layer="counts")
 
 celltypes = sorted(rna.obs['celltype'].unique())
@@ -55,12 +59,12 @@ rna_color_map = {celltype + '_rna': colors[i] for i, celltype in enumerate(cellt
 color_map = {**color_map, **sorted_color_map, **rna_color_map}
 color_map['Other'] = 'gray'
 
-hic = ad.read_h5ad(f"hic.h5ad")
+hic = ad.read_h5ad(hic_file)
 print(hic)
 print('Loading prior knowledge graph...')
-prior = nx.read_graphml(f"{prior_name}_prior_{resolution}_{suffix}.graphml.gz")
+prior = nx.read_graphml(graph_file)
 scglue.models.configure_dataset(hic, "NB", use_highly_variable=True)
-glue = scglue.models.load_model(f"glue_hic_{prior_name}_prior_{resolution}_{suffix}.dill")
+glue = scglue.models.load_model(model_file)
 
 
 genes = []