genal-python 1.3.0__tar.gz → 1.3.1__tar.gz

{genal_python-1.3.0 → genal_python-1.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: genal-python
-Version: 1.3.0
+Version: 1.3.1
 Summary: A python toolkit for polygenic risk scoring and mendelian randomization.
 Author-email: Cyprien Rivier <riviercyprien@gmail.com>
 Requires-Python: >=3.8
@@ -72,7 +72,7 @@ Genal is a python module designed to make it easy and intuitive to run genetic r
 - **Comprehensive MR Pipeline**: From data preprocessing to sensitivity analyses and plotting in a single package
 - **Reference Panel Support**: Automatically download and use the latest 1000 Genomes reference panels in builds 37 and 38 with the option to use custom reference panels
 - **Customizable**: Ability to choose all the parameters, but defaults are set to the most common values
-- **Proxy SNP Support**: Includes functionality for finding and using proxy SNPs when instruments are missing (for polygenic risk scores, Mendelian Randomization, and association testing)
+- **Proxy SNP Support**: Includes functionality for finding and using proxy SNPs when instruments are missing (for polygenic risk scores, Mendelian Randomization)
 
 The objective of genal is to bring the functionalities of well-established R packages such as TwoSampleMR, MR-Presso, MendelianRandomization, and gwasvcf, in a more user-friendly Python environment. This approach ensures that users have access to tried and tested techniques with the versatility of Python's data science tools. 
 

{genal_python-1.3.0 → genal_python-1.3.1}/README.md

@@ -47,7 +47,7 @@ Genal is a python module designed to make it easy and intuitive to run genetic r
 - **Comprehensive MR Pipeline**: From data preprocessing to sensitivity analyses and plotting in a single package
 - **Reference Panel Support**: Automatically download and use the latest 1000 Genomes reference panels in builds 37 and 38 with the option to use custom reference panels
 - **Customizable**: Ability to choose all the parameters, but defaults are set to the most common values
-- **Proxy SNP Support**: Includes functionality for finding and using proxy SNPs when instruments are missing (for polygenic risk scores, Mendelian Randomization, and association testing)
+- **Proxy SNP Support**: Includes functionality for finding and using proxy SNPs when instruments are missing (for polygenic risk scores, Mendelian Randomization)
 
 The objective of genal is to bring the functionalities of well-established R packages such as TwoSampleMR, MR-Presso, MendelianRandomization, and gwasvcf, in a more user-friendly Python environment. This approach ensures that users have access to tried and tested techniques with the versatility of Python's data science tools. 
 

{genal_python-1.3.0 → genal_python-1.3.1}/genal/Geno.py

@@ -42,8 +42,10 @@ from .colocalization import coloc_abf_func
 # Add proxying function (input is df + searchspace (list of SNP or path to .bim, can be separated by chromosomes) and returns proxied df)
 # Get proxies (simply return a list of proxies)
 # Include proxying option to association_test
-# Multi-MR
+# Multivariable-MR
 # Check stability with variants on sexual chromosomes
+# Check the build of user data (potentially with a list of SNPs with different positions)
+# update_snpids function: take alleles into account during the merge if they are present in the user data
 
 
 class Geno:
@@ -154,7 +156,7 @@ class Geno:
     def preprocess_data(
         self,
         preprocessing='Fill',
-        reference_panel="38",
+        reference_panel="37",
         effect_column=None,
         keep_indel=None,
         keep_dups=None,
@@ -290,7 +292,7 @@ class Geno:
 
         self.data = data
 
-    def get_reference_panel(self, reference_panel="38"):
+    def get_reference_panel(self, reference_panel="37"):
         """
         Retrieve or set the reference panel for the Geno object.
 

{genal_python-1.3.0 → genal_python-1.3.1}/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__ = "1.3.0"
+__version__ = "1.3.1"
 
 config_path = os.path.join(CONFIG_DIR, "config.json")
 

{genal_python-1.3.0 → genal_python-1.3.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "flit_core.buildapi"
 
 [project]
 name = "genal-python"  # Updated name for PyPI
-version = "1.3.0"
+version = "1.3.1"
 authors = [{name = "Cyprien Rivier", email = "riviercyprien@gmail.com"}]
 description = "A python toolkit for polygenic risk scoring and mendelian randomization."
 readme = "README.md"