geney 1.2.38__py2.py3-none-any.whl → 1.2.40__py2.py3-none-any.whl

geney/oncosplice.py

@@ -382,7 +382,7 @@ def oncosplice(mut_id, splicing_threshold=0.5, protein_coding=True, primary_tran
 
         assert len(ref_protein) == len(cons_vector), f"Protein ({len(ref_protein)}) and conservation vector ({len(cons_vector)}) must be same length. {ref_protein}, \n>{cons_vector}\n>{transcript.cons_seq}"
 
-        missplicing = Missplicing(find_transcript_missplicing(transcript, mutations, engine=engine), threshold=splicing_threshold)
+        missplicing = Missplicing(find_transcript_missplicing(transcript, mutations, engine=engine, threshold=splicing_threshold), threshold=splicing_threshold)
         for mutation in mutations:
             transcript.pre_mrna += mutation
 

geney/pangolin_utils.py

@@ -49,6 +49,7 @@ def pang_one_hot_encode(seq):
 def pangolin_predict_probs(true_seq, models):
     # print(f"Running pangolin on: {true_seq}")
     model_nums = [0, 2, 4, 6]
+    model_nums = [0, 1, 2, 3, 4, 5, 6]
     INDEX_MAP = {0: 1, 1: 2, 2: 4, 3: 5, 4: 7, 5: 8, 6: 10, 7: 11}
 
     # seq = 'N'*5000 + true_seq + 'N'*5000
@@ -73,10 +74,7 @@ def pangolin_predict_probs(true_seq, models):
 
         scores.append(np.mean(score, axis=0))
 
-    # splicing_pred = np.array(scores).max(axis=0)
-    splicing_pred = np.array(scores).mean(axis=0)
+    splicing_pred = np.array(scores).max(axis=0)
     donor_probs = [splicing_pred[i] * donor_dinucleotide[i] for i in range(len(true_seq))]
     acceptor_probs = [splicing_pred[i] * acceptor_dinucleotide[i] for i in range(len(true_seq))]
-    # print(acceptor_probs)
-    # return donor_probs[context:-context], acceptor_probs[context:-context]
     return donor_probs, acceptor_probs

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-1.2.38.dist-info → geney-1.2.40.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.2.38
+Version: 1.2.40
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.2.38.dist-info → geney-1.2.40.dist-info}/RECORD

@@ -6,21 +6,21 @@ geney/graphic_utils.py,sha256=tjm6IDQ1BdfSeuPYzjlqAUHFQoDYH9jXTzJjKFS4Hh4,11078
 geney/gtex_utils.py,sha256=asL2lHyU5KsbWpV096vkf1Ka7hSo_RRfZqw7p5nERmE,1919
 geney/immune_utils.py,sha256=ZRni5ttrhpYBnmNr0d0ZatIbNPYs4nmQuoUO00SpsS4,5271
 geney/mutation_utils.py,sha256=C_kv2MB_L8LlhX3W2ooXjJ3uDoJ8zX1WeDtZKoBZJkI,1547
-geney/oncosplice.py,sha256=Ph8AMR2L9wjh3Gl3X58Dd8F1ea4on9jXIxg7EO0zVEU,22565
-geney/pangolin_utils.py,sha256=ETTGpuaQgdZ1v8H0NP8sbTEfGWu0VXUFUS7wsURsTc4,2991
+geney/oncosplice.py,sha256=J_nFs_xBSJtgMqeHv628QodRL0B2d-Zi1Ke7Pk7S4R4,22595
+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-1.2.38.dist-info/METADATA,sha256=a5g8X4PPpand3B4nvkbemKP4Sj066AVa7AqIjLBEGSU,948
-geney-1.2.38.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
-geney-1.2.38.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.2.38.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,,