geney 1.2.9__py2.py3-none-any.whl → 1.2.11__py2.py3-none-any.whl

geney/oncosplice.py

@@ -519,6 +519,7 @@ class Transcript:
         seq, indices = self.pull_pre_mrna_pos()
         if self.variations:
             for mutation in self.variations.variants:
+                print(f"Implementing {mutation}")
                 seq, indices = generate_mut_variant(seq, indices, mut=mutation)
         return seq, indices
 
@@ -791,6 +792,7 @@ def find_transcript_missplicing(mutations, ref_transcript, var_transcript, conte
     start_pad, end_pad = max(0, context - (center_index - start_cutoff)), max(0, context - (end_cutoff - center_index))
     mut_seq = 'N' * start_pad + mut_seq[start_cutoff:end_cutoff] + 'N' * end_pad
     mut_indices = [-1] * start_pad + mut_indices[start_cutoff:end_cutoff] + [-1] * end_pad
+    print(mut_seq)
 
     copy_mut_indices = mut_indices.copy()
 
@@ -820,6 +822,9 @@ def find_transcript_missplicing(mutations, ref_transcript, var_transcript, conte
     visible_acceptors = np.intersect1d(ref_transcript.acceptors, ref_indices)
     # print(ref_indices.index(visible_donors[0]), ref_seq_donor_probs[ref_indices.index(visible_donors[0])], mut_seq_donor_probs[mut_indices.index(visible_donors[0])])
 
+    print(len(ref_seq_donor_probs), len(ref_seq_acceptor_probs), len(mut_seq_donor_probs), len(mut_seq_acceptor_probs), len(ref_indices), len(mut_indices))
+    print(ref_seq_donor_probs)
+
     assert len(ref_indices) == len(ref_seq_acceptor_probs), 'Reference pos not the same'
     assert len(mut_indices) == len(mut_seq_acceptor_probs), 'Mut pos not the same'
 
@@ -848,7 +853,9 @@ def find_transcript_missplicing(mutations, ref_transcript, var_transcript, conte
 
     missplicing = {'missed_acceptors': dap, 'missed_donors': ddp, 'discovered_acceptors': iap, 'discovered_donors': idp}
     missplicing = {outk: {float(k): v for k, v in outv.items()} for outk, outv in missplicing.items()}
-    return {outk: {int(k) if k.is_integer() else k: v for k, v in outv.items()} for outk, outv in missplicing.items()}
+    temp =  {outk: {int(k) if k.is_integer() else k: v for k, v in outv.items()} for outk, outv in missplicing.items()}
+    print(temp)
+    return temp
 
 
 # def run_spliceai_transcript(mutations, transcript_data, sai_mrg_context=5000, min_coverage=2500, sai_threshold=0.5, engine='spliceai'):

{geney-1.2.9.dist-info → geney-1.2.11.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.2.9
+Version: 1.2.11
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.2.9.dist-info → geney-1.2.11.dist-info}/RECORD

@@ -9,7 +9,7 @@ geney/gtex.py,sha256=asL2lHyU5KsbWpV096vkf1Ka7hSo_RRfZqw7p5nERmE,1919
 geney/gtex_utils.py,sha256=asL2lHyU5KsbWpV096vkf1Ka7hSo_RRfZqw7p5nERmE,1919
 geney/immune_utils.py,sha256=ZRni5ttrhpYBnmNr0d0ZatIbNPYs4nmQuoUO00SpsS4,5271
 geney/netchop.py,sha256=AMiy9YsdTmX4B3k3Y5Yh7EmoGAojM1O3AzhPKOiB--g,3050
-geney/oncosplice.py,sha256=8No5m_ZbDy2yeBXMrFWPKwuVwZFugfEBYA1NEpvNZzk,77465
+geney/oncosplice.py,sha256=ZaCsRUNLhGx3Yg9l-Vp7MnP4_mOe3fj6T-_d9Wfs1QE,77755
 geney/oncosplice_mouse.py,sha256=LYLOukI9qI1IBkyl1qVRFR5d1NAw7Orlj8Zth-4xCW8,12962
 geney/oncosplice_pipeline.py,sha256=hpGqFHOdn8i8tvvs1-t3-G9Ko18zInwoDXBJbbrfbC4,68036
 geney/performance_utils.py,sha256=FQt7rA4r-Wuq3kceCxsSuMfj3wU1tMG8QnbL59aBohs,4700
@@ -45,7 +45,7 @@ geney/translation_initiation/resources/kozak_pssm.json,sha256=pcd0Olziutq-6H3mFW
 geney/translation_initiation/resources/tis_regressor_model.joblib,sha256=IXb4DUDhJ5rBDKcqMk9zE3ECTZZcdj7Jixz3KpoZ7OA,2592025
 geney/translation_termination/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 geney/translation_termination/tts_utils.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-geney-1.2.9.dist-info/METADATA,sha256=c2sjvZk1ElBTxFmxYXCSgz2d9pidaMcAXAWVCV0r7DA,1198
-geney-1.2.9.dist-info/WHEEL,sha256=iYlv5fX357PQyRT2o6tw1bN-YcKFFHKqB_LwHO5wP-g,110
-geney-1.2.9.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.2.9.dist-info/RECORD,,
+geney-1.2.11.dist-info/METADATA,sha256=Ll6Nz8fBNL_ZIVWYxb8NnWlt1AIKQoNOazopm6c6q-I,1199
+geney-1.2.11.dist-info/WHEEL,sha256=iYlv5fX357PQyRT2o6tw1bN-YcKFFHKqB_LwHO5wP-g,110
+geney-1.2.11.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.2.11.dist-info/RECORD,,