geney 1.2.51__py2.py3-none-any.whl → 1.2.53__py2.py3-none-any.whl

geney/oncosplice.py

@@ -421,7 +421,7 @@ import asyncio
 
 
 async def oncosplice_prototype(mut_id, splicing_threshold=0.5, protein_coding=True, primary_transcript=False,
-                               window_length=13, organism='hg38', engine='spliceai'):
+                               window_length=13, organism='hg38', engine='spliceai', use_cons=True):
     import sys, os
     needed_file1 = config[organism]['yoram_path'] / 'rest_api_utils.py'
     needed_file2 = config[organism]['yoram_path'] / 'uniprot_utils.py'
@@ -470,6 +470,10 @@ async def oncosplice_prototype(mut_id, splicing_threshold=0.5, protein_coding=Tr
         transcript.cons_vector = transform_conservation_vector(transcript.cons_vector, window=window_length)
         transcript.generate_mature_mrna().generate_protein(inplace=True)
         ref_protein, cons_vector = transcript.protein, transcript.cons_vector
+
+        if not use_cons:
+            cons_vector = np.ones(len(ref_protein))
+
         if sum(cons_vector) == 0:
             cons_vector = np.ones(len(ref_protein))/len(ref_protein)
 

geney/pangolin_utils.py

@@ -56,7 +56,8 @@ def pangolin_predict_probs(true_seq, models):
     seq = true_seq
     true_seq = true_seq[5000:-5000]
     acceptor_dinucleotide = np.array([true_seq[i - 2:i] == 'AG' for i in range(len(true_seq))])
-    donor_dinucleotide = np.array([true_seq[i + 1:i + 3] == 'GT' for i in range(len(true_seq))])
+    # donor_dinucleotide = np.array([true_seq[i + 1:i + 3] == 'GT' for i in range(len(true_seq))])
+    donor_dinucleotide = np.array([true_seq[i -2:i] == 'GT' for i in range(len(true_seq))])
 
     seq = pang_one_hot_encode(seq).T
     seq = torch.from_numpy(np.expand_dims(seq, axis=0)).float()

geney/splicing_utils.py

@@ -150,17 +150,10 @@ def find_ss_changes(ref_dct, mut_dct, known_splice_sites, threshold=0.5):
 
 def find_transcript_missplicing(transcript, mutations, context=5000, window=2500, threshold=0.5, engine='spliceai'):
     from functools import reduce
-
     ref = transcript.pre_mrna
-    # for mutation in mutations:
-    #     var = ref + mutation
-
     var = reduce(lambda acc, mutation: acc + mutation, mutations, ref)
-
     center = int(np.mean([mutation.position for mutation in mutations]) // 1)
-
     total_context = context + window
-
     length = ref.seqmat.shape[-1]
     center_index = ref.rel_pos(center)
     ref_start_pad = max(0, total_context - center_index)
@@ -173,9 +166,6 @@ def find_transcript_missplicing(transcript, mutations, context=5000, window=2500
 
     ref = ref.inspect(center, context=total_context)
     var = var.inspect(center, context=total_context)
-    #
-    # ref_indices = np.concatenate([np.zeros(ref_start_pad), ref.inspect(center, context = window).indices, np.zeros(ref_end_pad)])
-    # mut_indices = np.concatenate([np.zeros(var_start_pad), var.inspect(center, context = window).indices, np.zeros(var_end_pad)])
 
     ref_indices = np.concatenate([np.zeros(ref_start_pad), ref.indices, np.zeros(ref_end_pad)])
     mut_indices = np.concatenate([np.zeros(var_start_pad),  var.indices, np.zeros(var_end_pad)])
@@ -186,13 +176,12 @@ def find_transcript_missplicing(transcript, mutations, context=5000, window=2500
     ref_seq = 'N'*ref_start_pad + ref.seq + 'N'*ref_end_pad
     var_seq = 'N'*var_start_pad + var.seq + 'N'*var_end_pad
 
-    # print(f"PAdding: {ref_start_pad}, {ref_end_pad}")
+    print(ref_seq)
+
     if engine == 'spliceai':
         from .spliceai_utils import sai_predict_probs, sai_models
         ref_seq_acceptor_probs, ref_seq_donor_probs = sai_predict_probs(ref_seq, models=sai_models)
         mut_seq_acceptor_probs, mut_seq_donor_probs = sai_predict_probs(var_seq, models=sai_models)
-        # ref_seq_acceptor_probs, ref_seq_donor_probs = ref_seq_probs_temp[0, :], ref_seq_probs_temp[1, :]
-        # mut_seq_acceptor_probs, mut_seq_donor_probs = mut_seq_probs_temp[0, :], mut_seq_probs_temp[1, :]
 
     elif engine == 'pangolin':
         from .pangolin_utils import pangolin_predict_probs, pang_models

{geney-1.2.51.dist-info → geney-1.2.53.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.2.51
+Version: 1.2.53
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.2.51.dist-info → geney-1.2.53.dist-info}/RECORD

@@ -6,12 +6,12 @@ geney/graphic_utils.py,sha256=oMsBpB9YeEn96gGpKh4MmtagJffWZbk-xPrIwHvkFhA,11016
 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=nP8SEXvaZbU-K_pzIOKJ6BNAl3QJgidRiptm7xBzACM,23440
-geney/pangolin_utils.py,sha256=lLmnjJdJjqwWS85-1jlPLIjD2z14sWjzU87hS-8xxpQ,2873
+geney/oncosplice.py,sha256=hPmB9sEPs9lr22BlPGKpQUOd59vUjAttXZ6QKf4A-kg,23534
+geney/pangolin_utils.py,sha256=rVi_U23nhw6wCc44fBeD3sv-FshLTGE1UMMtIYwgr9U,2967
 geney/power_utils.py,sha256=MehZFUdkJ2EFUot709yPEDxSkXmH5XevMebX2HD768A,7330
 geney/seqmat_utils.py,sha256=2cRXT_Ox4IdzCM8x3H2HexxFZzjo5WHs0HZiUQv8fBM,18347
 geney/spliceai_utils.py,sha256=gIGPC8u3J15A7EQrk2Elho5PbF9MmUUNopGGH-eEV8s,1873
-geney/splicing_utils.py,sha256=lGBNknnAdKhcJ3MqPQ5c9oz_NKcL2lcFAr78StjKa6o,16151
+geney/splicing_utils.py,sha256=GpzvdXKBawTXp8SUJiC9aGV3_RX7LzkkUfk4_kdu5rI,15562
 geney/survival_utils.py,sha256=FKcXGL7FNp9yuVyNaUudVgn-JBuZfrhvS1c1NZE-tZ4,6880
 geney/tcga_utils.py,sha256=D_BNHm-D_K408dlcJm3hzH2c6QNFjQsKvUcOPiQRk7g,17612
 geney/tis_utils.py,sha256=vA2ci4gNfwwQZlCjPpO5ehvL2NRVeM7lHI_VyfT-_10,8049
@@ -20,7 +20,7 @@ geney/translation_initiation/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NM
 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-1.2.51.dist-info/METADATA,sha256=E_TbmjJ5ylFzUqgTAEFmL9ARawLGuFH9wzZ0fUMltOQ,948
-geney-1.2.51.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
-geney-1.2.51.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.2.51.dist-info/RECORD,,
+geney-1.2.53.dist-info/METADATA,sha256=o8uT_lpsOsrQyXfD84OkN-EFUaVJGmo18IOQK75cUjw,948
+geney-1.2.53.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
+geney-1.2.53.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.2.53.dist-info/RECORD,,