geney 1.2.39__py2.py3-none-any.whl → 1.2.40__py2.py3-none-any.whl

geney/splicing_utils.py

@@ -139,11 +139,11 @@ def find_ss_changes(ref_dct, mut_dct, known_splice_sites, threshold=0.5):
     new_dict = {v: mut_dct.get(v, 0) - ref_dct.get(v, 0) for v in
                 list(set(list(ref_dct.keys()) + list(mut_dct.keys())))}
 
-    discovered_pos = {k: {'delta': round(float(v), 3), 'absolute': round(float(mut_dct[k]), 3)} for k, v in
-                      new_dict.items() if v >= threshold and k not in known_splice_sites}   # if (k not in known_splice_sites and v >= threshold) or (v > 0.45)}
+    discovered_pos = {k: {'delta': round(float(v), 3), 'absolute': round(float(mut_dct[k]), 3), 'reference': round(ref_dct[k], 3)} for k, v in
+                      new_dict.items() if v >= threshold} # and k not in known_splice_sites}   # if (k not in known_splice_sites and v >= threshold) or (v > 0.45)}
 
-    deleted_pos = {k: {'delta': round(float(v), 3), 'absolute': round(float(mut_dct.get(k, 0)), 3)} for k, v in
-                   new_dict.items() if -v >= threshold and k in known_splice_sites}      #if k in known_splice_sites and v <= -threshold}
+    deleted_pos = {k: {'delta': round(float(v), 3), 'absolute': round(float(mut_dct.get(k, 0)), 3), 'reference': round(ref_dct[k], 3)} for k, v in
+                   new_dict.items() if -v >= threshold} # and k in known_splice_sites}      #if k in known_splice_sites and v <= -threshold}
 
     return discovered_pos, deleted_pos
 

geney/tis_utils.py

@@ -133,7 +133,7 @@ def build_titer_model(TITER_path=config['hg38']['titer_path']):
         if os.path.exists(weights_path):
             model_copy.load_weights(weights_path)  # Load weights into the new model instance
             models.append(model_copy)
-            print(f"Loaded model {i} with weights from {weights_path}")
+            # print(f"Loaded model {i} with weights from {weights_path}")
         else:
             print(f"Warning: Weights file {weights_path} not found")
 

{geney-1.2.39.dist-info → geney-1.2.40.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.2.39
+Version: 1.2.40
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.2.39.dist-info → geney-1.2.40.dist-info}/RECORD

@@ -11,16 +11,16 @@ geney/pangolin_utils.py,sha256=lLmnjJdJjqwWS85-1jlPLIjD2z14sWjzU87hS-8xxpQ,2873
 geney/power_utils.py,sha256=MehZFUdkJ2EFUot709yPEDxSkXmH5XevMebX2HD768A,7330
 geney/seqmat_utils.py,sha256=YV5DFLbfjXLIswPGvqK1-eEfwn9TUby0b2kewdGAKws,18372
 geney/spliceai_utils.py,sha256=gIGPC8u3J15A7EQrk2Elho5PbF9MmUUNopGGH-eEV8s,1873
-geney/splicing_utils.py,sha256=q47EdcsHrp4aLIPVWvkGBJSzS3l3DKiD9DNDsPpZdHk,16075
+geney/splicing_utils.py,sha256=lGBNknnAdKhcJ3MqPQ5c9oz_NKcL2lcFAr78StjKa6o,16151
 geney/survival_utils.py,sha256=2CAkC2LsspicHIdrqsiPnjgvpr5KHDUfLFFqnRbPJqs,5762
 geney/tcga_utils.py,sha256=vXSMf1OxoF_AdE_rMguy_BoYaart_E1t4FFMx2DS1Ak,15585
-geney/tis_utils.py,sha256=Oz54dgAjc1PEikp4Snh6qlpT-8eVJDWhM_k0aJAQvFM,8047
+geney/tis_utils.py,sha256=vA2ci4gNfwwQZlCjPpO5ehvL2NRVeM7lHI_VyfT-_10,8049
 geney/utils.py,sha256=EsKvBM-Nz2a3_4ZAhF4Dxd4PwT7_6YYKpxEN4LLgg10,2174
 geney/translation_initiation/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 geney/translation_initiation/tis_utils.py,sha256=AF3siFjuQH-Rs44EV-80zHdbxRMvN4woLFSHroWIETc,4448
 geney/translation_initiation/resources/kozak_pssm.json,sha256=pcd0Olziutq-6H3mFWDCD9cujQ_AlZO-iiOvBl82hqE,1165
 geney/translation_initiation/resources/tis_regressor_model.joblib,sha256=IXb4DUDhJ5rBDKcqMk9zE3ECTZZcdj7Jixz3KpoZ7OA,2592025
-geney-1.2.39.dist-info/METADATA,sha256=i-1cERTVvL1H3UBw9RJbGNT6KaySdTAAHhXxL9mEo4M,948
-geney-1.2.39.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
-geney-1.2.39.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.2.39.dist-info/RECORD,,
+geney-1.2.40.dist-info/METADATA,sha256=ja7ULYnyNPbYYj-wloXQzHDH86TL2mg4LfgEmZaMcbE,948
+geney-1.2.40.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
+geney-1.2.40.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.2.40.dist-info/RECORD,,