geney 1.2.18__py2.py3-none-any.whl → 1.2.20__py2.py3-none-any.whl

geney/__init__.py

@@ -1,6 +1,6 @@
 from .config_setup import get_config
 config_setup = get_config()
-
+print("Hello Geney.")
 # import os
 # import json
 # from pathlib import Path

geney/oncosplice.py

@@ -12,8 +12,7 @@ import matplotlib.pyplot as plt
 from matplotlib.patches import Rectangle
 import seaborn as sns
 from collections import namedtuple
-
-
+print('hellp')
 from geney.utils import find_files_by_gene_name, reverse_complement, unload_pickle, contains, unload_json, dump_json #, is_monotonic
 from geney.Fasta_segment import Fasta_segment
 
@@ -29,7 +28,6 @@ tf.config.threading.set_inter_op_parallelism_threads(1)
 sai_paths = ('models/spliceai{}.h5'.format(x) for x in range(1, 6))
 sai_models = [load_model(resource_filename('spliceai', x)) for x in sai_paths]
 
-
 # Load models
 import torch
 from pkg_resources import resource_filename
@@ -50,15 +48,21 @@ for i in pang_model_nums:
         model.eval()
         pang_models.append(model)
 
+
+# def is_monotonic(A):
+#     x, y = [], []
+#     x.extend(A)
+#     y.extend(A)
+#     x.sort()
+#     y.sort(reverse=True)
+#     if (x == A or y == A):
+#         return True
+#     return False
+
+
 def is_monotonic(A):
-    x, y = [], []
-    x.extend(A)
-    y.extend(A)
-    x.sort()
-    y.sort(reverse=True)
-    if (x == A or y == A):
-        return True
-    return False
+    return all(x <= y for x, y in zip(A, A[1:])) or all(x >= y for x, y in zip(A, A[1:]))
+
 
 def sai_predict_probs(seq: str, models: list) -> list:
     '''
@@ -1022,7 +1026,7 @@ def find_transcript_missplicing(mutations, ref_transcript, var_transcript, conte
 
 class PredictSpliceAI:
     def __init__(self, mutation, gene_data,
-                threshold=0.5, force=False,  save_results=False, sai_mrg_context=5000, min_coverage=2500, engine='spliceai'):
+                threshold=0.5, force=False,  save_results=False, sai_mrg_context=5000, min_coverage=2500, engine='spliceai', organism='hg38'):
         self.modification = mutation
         self.threshold = threshold
         self.transcript_id = gene_data.transcript_id
@@ -1043,7 +1047,7 @@ class PredictSpliceAI:
 
             # self.missplicing = run_spliceai_transcript(self.modification, transcript_data=gene_data, sai_mrg_context=sai_mrg_context, min_coverage=min_coverage, sai_threshold=0.1)
             # print(f"RUNNING: {mutation.mut_id}")
-            ref_transcript, var_transcript = Gene(mutation.mut_id.split(':')[0], organism='mm39').transcript(gene_data.transcript_id), Gene(mutation.mut_id.split(':')[0], mutation.mut_id, organism='mm39').transcript(gene_data.transcript_id)
+            ref_transcript, var_transcript = Gene(mutation.mut_id.split(':')[0], organism=organism).transcript(gene_data.transcript_id), Gene(mutation.mut_id.split(':')[0], mutation.mut_id, organism='mm39').transcript(gene_data.transcript_id)
             # print(f"Second check : {ref_transcript.pre_mrna == var_transcript.pre_mrna}")
             self.missplicing = find_transcript_missplicing(self.modification, ref_transcript, var_transcript, context=sai_mrg_context+min_coverage, threshold=threshold,
                                 engine=engine)
@@ -1531,7 +1535,7 @@ def oncosplice(mut_id, sai_threshold=0.5, protein_coding=True, primary_transcrip
             continue
 
         cons_vector = transform_conservation_vector(reference.cons_vector, window=window_length)
-        missplicing_obj = PredictSpliceAI(mutation, reference, threshold=sai_threshold, force=force_spliceai, save_results=save_spliceai_results, engine=engine)
+        missplicing_obj = PredictSpliceAI(mutation, reference, threshold=sai_threshold, force=force_spliceai, save_results=save_spliceai_results, engine=engine, organism=organism)
         missplicing = missplicing_obj.apply_sai_threshold_primary(threshold=sai_threshold)
 
         for i, new_boundaries in enumerate(develop_aberrant_splicing(variant, missplicing)):

geney/power_utils.py

@@ -12,6 +12,7 @@ import gc
 import pandas as pd
 import argparse
 
+print("remote this")
 tqdm.pandas()
 warnings.filterwarnings('ignore')
 

{geney-1.2.18.dist-info → geney-1.2.20.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.2.18
+Version: 1.2.20
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.2.18.dist-info → geney-1.2.20.dist-info}/RECORD

@@ -1,6 +1,6 @@
 geney/Fasta_segment.py,sha256=0zCdzPUbDeM9Rz642woH5Q94pwI46O0fE3H8w0XWebc,11255
 geney/Gene.py,sha256=abHnvZ4ytbjQmoBtrbsX5G0QAspm06NqZBINkjHgPog,10140
-geney/__init__.py,sha256=r-Yvpo_Tc236DcsqsFyexT21iVoYCVl9zoJj5pFuWEE,407
+geney/__init__.py,sha256=knezxgbV2c2gcO2ek2-xxEC15HL4aO1WuoMiYOOvKf8,428
 geney/benchmark_clinvar.py,sha256=LLl77e95Qbg9Kd-m2yL8ilmzubSz9SKogeARwssT4Ks,5532
 geney/compare_sets.py,sha256=TcgL57V7BUPxBoW9lv3xr8qK2Acmykn85Ev3avicQr8,2977
 geney/config_setup.py,sha256=VA6mhVGMRadwlpEx4m1wrssmDM8qpfKT21MAijIwjyQ,428
@@ -9,11 +9,11 @@ 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=MA8z8D2kZCrIeXJwu0D6rM_VvryldvkNkzETkE29cts,78057
+geney/oncosplice.py,sha256=sp6kfKbFqwpZIuLZadvCq0aj-JUnM_GE99eaGRm19eY,78240
 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
-geney/power_utils.py,sha256=_B5DIKfwQGb1Gy9xbIUrOCiTf5y_Nq10OMtaFjEo3i8,7309
+geney/power_utils.py,sha256=MehZFUdkJ2EFUot709yPEDxSkXmH5XevMebX2HD768A,7330
 geney/survival.py,sha256=gNKZGcwxDZ00ixVBHf3ZdjbY_AHQOCU9kKpBC_dokbM,5572
 geney/survival_utils.py,sha256=2CAkC2LsspicHIdrqsiPnjgvpr5KHDUfLFFqnRbPJqs,5762
 geney/tcga_annotations.py,sha256=DjRl6Pk5VAOL1yhbt8SXD6FZhYbcYNu3FtXYMeveGB0,15016
@@ -46,7 +46,7 @@ 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-1.2.18.dist-info/METADATA,sha256=TR4c2Ytss-agQ850EcaSjgKkHqbC0VsMsRxNnnUxEHU,1163
-geney-1.2.18.dist-info/WHEEL,sha256=iYlv5fX357PQyRT2o6tw1bN-YcKFFHKqB_LwHO5wP-g,110
-geney-1.2.18.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.2.18.dist-info/RECORD,,
+geney-1.2.20.dist-info/METADATA,sha256=YRkn1hq4ARDlqMiAWPpDmbUny5v7NxjbN4YcRpaq2o8,1163
+geney-1.2.20.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
+geney-1.2.20.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.2.20.dist-info/RECORD,,

{geney-1.2.18.dist-info → geney-1.2.20.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.41.2)
+Generator: setuptools (75.1.0)
 Root-Is-Purelib: true
 Tag: py2-none-any
 Tag: py3-none-any