genal-python 1.2.7__tar.gz → 1.2.8__tar.gz

{genal_python-1.2.7 → genal_python-1.2.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: genal-python
-Version: 1.2.7
+Version: 1.2.8
 Summary: A python toolkit for polygenic risk scoring and mendelian randomization.
 Author-email: Cyprien Rivier <riviercyprien@gmail.com>
 Requires-Python: >=3.8

{genal_python-1.2.7 → genal_python-1.2.8}/genal/Geno.py

@@ -495,9 +495,9 @@ class Geno:
             path=None, 
             proxy=False,
             reference_panel="eur",
-            kb=5000,
+            kb=10000,
             r2=0.6,
-            window_snps=5000,
+            window_snps=10000,
             
            ):
         """
@@ -767,9 +767,9 @@ class Geno:
         name=None,
         proxy=True,
         reference_panel="eur",
-        kb=5000,
+        kb=10000,
         r2=0.6,
-        window_snps=5000,
+        window_snps=10000,
     ):
         """
         Prepares dataframes required for Mendelian Randomization (MR) with the SNP information in `data` as exposure.

{genal_python-1.2.7 → genal_python-1.2.8}/genal/__init__.py

@@ -4,7 +4,7 @@ from .tools import default_config, write_config, set_plink, install_plink, delet
 from .geno_tools import Combine_Geno
 from .constants import CONFIG_DIR
 
-__version__ = "1.2.7"
+__version__ = "1.2.8"
 
 config_path = os.path.join(CONFIG_DIR, "config.json")
 

{genal_python-1.2.7 → genal_python-1.2.8}/genal/extract_prs.py

@@ -139,7 +139,7 @@ def extract_snps_func(snp_list, name, path=None):
     #Check that at least 1 variant has been extracted. If not, return "FAILED" to warn downstream functions (prs, association_test)
     log_path = output_path + ".log"
     with open(log_path, 'r') as log_file:
-        if "0 variants remaining" in log_file.read():
+        if " 0 variants remaining" in log_file.read():
             print("None of the provided SNPs were found in the genetic data.")
             return "FAILED"
         else:

{genal_python-1.2.7 → genal_python-1.2.8}/genal/proxy.py

@@ -193,9 +193,9 @@ def find_proxies(
     snp_list,
     searchspace=None,
     reference_panel="eur",
-    kb=5000,
+    kb=10000,
     r2=0.6,
-    window_snps=5000,
+    window_snps=10000,
     threads=1
 ):
     """

{genal_python-1.2.7 → genal_python-1.2.8}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "flit_core.buildapi"
 
 [project]
 name = "genal-python"  # Updated name for PyPI
-version = "1.2.7"
+version = "1.2.8"
 authors = [{name = "Cyprien Rivier", email = "riviercyprien@gmail.com"}]
 description = "A python toolkit for polygenic risk scoring and mendelian randomization."
 readme = "README.md"