geney 1.1.18__py2.py3-none-any.whl → 1.2.1__py2.py3-none-any.whl

geney/config_setup.py

@@ -3,9 +3,9 @@ import json
 from pathlib import Path
 
 def get_config():
-    config_file = os.path.join(os.path.expanduser('~'), '.oncosplice_setup', 'config.json')
+    config_file = os.path.join(os.path.expanduser('~'), '.oncosplice_setup_1_2', 'config.json')
     if Path(config_file).exists():
-        config_setup = {k: Path(p) for k, p in json.loads(open(config_file).read()).items()}
+        config_setup = {k: {k_in: Path(p_in) for k_in, p_in in p.items()} for k, p in json.loads(open(config_file).read()).items()}
 
     else:
         print("Database not set up.")

geney/data_setup.py

@@ -135,7 +135,7 @@ def retrieve_and_parse_ensembl_annotations(local_path, annotations_file, cons_da
             biotype_path.mkdir()
 
         gene_attribute = gene_attribute.squeeze()
-        file_name = biotype_path / f'mrnas_{gene_id}_{gene_attribute.gene_name}.pkl'
+        file_name = biotype_path / f'mrnas_{gene_id}_{gene_attribute.gene_name.upper()}.pkl'
         if file_name.exists():
             continue
 
@@ -202,7 +202,7 @@ def write_sequence(output_directory, header, sequence):
 
 
 def main():
-    config_dir = Path(os.path.join(os.path.expanduser('~'), '.oncosplice_setup_new'))
+    config_dir = Path(os.path.join(os.path.expanduser('~'), '.oncosplice_setup_1_2'))
     # if config_dir.exists():
     #     for file in config_dir.glob('*'):
     #         file.unlink()
@@ -269,8 +269,8 @@ def main():
 
     cons_file = download(file_maps['cons_url'], base_path)
 
-    if file_maps['gtex_url']:
-        gtex_file = download_and_ungzip(file_maps['gtex_url'], base_path)
+    if file_maps['expression_url']:
+        gtex_file = download_and_ungzip(file_maps['expression_url'], base_path)
     else:
         gtex_file = None
 
@@ -289,7 +289,8 @@ def main():
         splicing_path.mkdir(parents=True)
 
     fasta_file.unlink()
-    gtex_file.unlink()
+    if gtex_file:
+        gtex_file.unlink()
     ensembl_file.unlink()
     cons_file.unlink()
     print(f"Finished mounding database in {args.basepath}.")

{geney-1.1.18.dist-info → geney-1.2.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.1.18
+Version: 1.2.1
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.1.18.dist-info → geney-1.2.1.dist-info}/RECORD

@@ -3,8 +3,8 @@ geney/Gene.py,sha256=abHnvZ4ytbjQmoBtrbsX5G0QAspm06NqZBINkjHgPog,10140
 geney/__init__.py,sha256=r-Yvpo_Tc236DcsqsFyexT21iVoYCVl9zoJj5pFuWEE,407
 geney/benchmark_clinvar.py,sha256=LLl77e95Qbg9Kd-m2yL8ilmzubSz9SKogeARwssT4Ks,5532
 geney/compare_sets.py,sha256=TcgL57V7BUPxBoW9lv3xr8qK2Acmykn85Ev3avicQr8,2977
-geney/config_setup.py,sha256=SePeooA4RWAtR_KAT1-W1hkD3MT5tH6YMyp80t_RNPQ,385
-geney/data_setup.py,sha256=eunGh_TAUtU2osxZkDEBGRgRHmhwAMoUBVw_f5LfqOo,12010
+geney/config_setup.py,sha256=VA6mhVGMRadwlpEx4m1wrssmDM8qpfKT21MAijIwjyQ,428
+geney/data_setup.py,sha256=mV_sSCMT8C41q_PD_G34MIBvsBKA0Czrpw17-DcYmT4,12052
 geney/gtex.py,sha256=asL2lHyU5KsbWpV096vkf1Ka7hSo_RRfZqw7p5nERmE,1919
 geney/gtex_utils.py,sha256=asL2lHyU5KsbWpV096vkf1Ka7hSo_RRfZqw7p5nERmE,1919
 geney/immune_utils.py,sha256=ZRni5ttrhpYBnmNr0d0ZatIbNPYs4nmQuoUO00SpsS4,5271
@@ -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-1.1.18.dist-info/METADATA,sha256=sSlG-zbp8HBnXdX00xesA29u0KJpGZmSXGwOaiszyFs,1199
-geney-1.1.18.dist-info/WHEEL,sha256=iYlv5fX357PQyRT2o6tw1bN-YcKFFHKqB_LwHO5wP-g,110
-geney-1.1.18.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.1.18.dist-info/RECORD,,
+geney-1.2.1.dist-info/METADATA,sha256=HgySFYXNAhqjuBEJU8_I5oSKq2Rf6v-0hNIQmaqKbEE,1198
+geney-1.2.1.dist-info/WHEEL,sha256=iYlv5fX357PQyRT2o6tw1bN-YcKFFHKqB_LwHO5wP-g,110
+geney-1.2.1.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.2.1.dist-info/RECORD,,