geney 1.2.52__py2.py3-none-any.whl → 1.2.54__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', cons_vector=True):
+                               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'
@@ -471,7 +471,7 @@ async def oncosplice_prototype(mut_id, splicing_threshold=0.5, protein_coding=Tr
         transcript.generate_mature_mrna().generate_protein(inplace=True)
         ref_protein, cons_vector = transcript.protein, transcript.cons_vector
 
-        if not cons_vector:
+        if not use_cons:
             cons_vector = np.ones(len(ref_protein))
 
         if sum(cons_vector) == 0:

geney/splicing_utils.py

@@ -176,7 +176,7 @@ 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(ref_seq)
+    # print(ref_seq)
 
     if engine == 'spliceai':
         from .spliceai_utils import sai_predict_probs, sai_models

geney/survival_utils.py

@@ -2,7 +2,7 @@ import pandas as pd
 import numpy as np
 import matplotlib.pyplot as plt
 from pathlib import Path
-from scipy.integrate import trapz
+# from scipy.integrate import trapezoid
 from geney.utils import unload_pickle, unload_json, contains
 from lifelines.exceptions import ConvergenceError
 from lifelines import KaplanMeierFitter

{geney-1.2.52.dist-info → geney-1.2.54.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.2.52
+Version: 1.2.54
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.2.52.dist-info → geney-1.2.54.dist-info}/RECORD

@@ -6,13 +6,13 @@ 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=wYJeCED6QktO4eHdtc5eXxnbwiv1S3ysN33lWn-GMAI,23540
+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=GpzvdXKBawTXp8SUJiC9aGV3_RX7LzkkUfk4_kdu5rI,15562
-geney/survival_utils.py,sha256=FKcXGL7FNp9yuVyNaUudVgn-JBuZfrhvS1c1NZE-tZ4,6880
+geney/splicing_utils.py,sha256=8qbj81ESNxu9-clEjBV-2xj41p1Wly6NFiGlm0etSeg,15564
+geney/survival_utils.py,sha256=KnAzEviMuXh6SnVXId9PgsFLSbgkduTvYoIthxN7FPA,6886
 geney/tcga_utils.py,sha256=D_BNHm-D_K408dlcJm3hzH2c6QNFjQsKvUcOPiQRk7g,17612
 geney/tis_utils.py,sha256=vA2ci4gNfwwQZlCjPpO5ehvL2NRVeM7lHI_VyfT-_10,8049
 geney/utils.py,sha256=EsKvBM-Nz2a3_4ZAhF4Dxd4PwT7_6YYKpxEN4LLgg10,2174
@@ -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-1.2.52.dist-info/METADATA,sha256=3aWpix97X-XO5i1c6vDlbLpS0s7jAu2DbYdWTK9DPd8,948
-geney-1.2.52.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
-geney-1.2.52.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.2.52.dist-info/RECORD,,
+geney-1.2.54.dist-info/METADATA,sha256=C4gCBwzsS6uD4ZqO1lE5Me2BAldGdvBk50hQkp5C528,948
+geney-1.2.54.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
+geney-1.2.54.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.2.54.dist-info/RECORD,,