gwaslab 3.5.7__tar.gz → 3.6.0__tar.gz

{gwaslab-3.5.7/src/gwaslab.egg-info → gwaslab-3.6.0}/PKG-INFO

@@ -1,12 +1,12 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: gwaslab
-Version: 3.5.7
+Version: 3.6.0
 Summary: A collection of handy tools for GWAS SumStats
 Author-email: Yunye <yunye@gwaslab.com>
 Project-URL: Homepage, https://cloufield.github.io/gwaslab/
 Project-URL: Github, https://github.com/Cloufield/gwaslab
 Classifier: Programming Language :: Python :: 3
-Classifier: License :: OSI Approved :: MIT License
+Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
 Classifier: Operating System :: OS Independent
 Requires-Python: <3.13,>=3.9
 Description-Content-Type: text/markdown
@@ -25,52 +25,74 @@ Requires-Dist: scikit-allel>=1.3.5
 Requires-Dist: pyensembl==2.2.3
 Requires-Dist: gtfparse==1.3.0
 Requires-Dist: h5py>=3.10.0
+Dynamic: license-file
 
 # GWASLab
 
-<img width="600" alt="image" src="https://user-images.githubusercontent.com/40289485/197167760-5f761f5e-5856-4b27-a540-8b9cd90bdadb.png">
+<img width="600" alt="image" src="https://github.com/user-attachments/assets/109262c6-c870-4078-94b5-66cf8c6b13c4" />
 
 ![badge](https://img.shields.io/pypi/v/gwaslab)
 [![Downloads](https://static.pepy.tech/badge/gwaslab)](https://pepy.tech/project/gwaslab)
 ![badge_pip](https://img.shields.io/pypi/dm/gwaslab)
-[![Hits](https://hits.seeyoufarm.com/api/count/incr/badge.svg?url=https%3A%2F%2Fcloufield.github.io%2Fgwaslab%2F&count_bg=%2379C83D&title_bg=%23555555&icon=&icon_color=%23E7E7E7&title=hits&edge_flat=false)](https://hits.seeyoufarm.com)
 ![badge_commit_m](https://img.shields.io/github/commit-activity/m/Cloufield/gwaslab)
 
-* A handy Python toolkit for handling GWAS summary statistics (sumstats).
+* A handy Python-based toolkit for handling GWAS summary statistics (sumstats).
 * Each process is modularized and can be customized to your needs.
 * Sumstats-specific manipulations are designed as methods of a Python object, `gwaslab.Sumstats`.
 
-Please check GWASLab documentation at [https://cloufield.github.io/gwaslab/](https://cloufield.github.io/gwaslab/)
+## Installation
 
-Note: GWASLab is being updated very frequently for now. I will release the first stable version soon! Please stay tuned.
+### install via pip
 
-Warning: Known issues of GWASLab are summarized in [https://cloufield.github.io/gwaslab/KnownIssues/](https://cloufield.github.io/gwaslab/KnownIssues/) .
+The latest version of GWASLab now supports Python 3.9, 3.10, 3.11, and 3.12.
 
-## Install
+```bash
+pip install gwaslab
+```
 
-### install via pip
+### install in conda environment
+
+Create a Python 3.9, 3.10, 3.11 or 3.12 environment and install gwaslab using pip:
+
+```bash
+conda env create -n gwaslab -c conda-forge python=3.12
+
+conda activate gwaslab
 
+pip install gwaslab
 ```
-pip install gwaslab==3.5.4
+
+or create a new environment using yml file [environment.yml](https://github.com/Cloufield/gwaslab/blob/main/environment.yml)
+
+```bash
+conda env create -n gwaslab -f environment.yml
 ```
 
+### install using docker (deprecated)
+
+A docker file is available [here](https://github.com/Cloufield/gwaslab/blob/main/docker/Dockerfile) for building local images.
+
+## Quick start
+
 ```python
+
 import gwaslab as gl
+
 # load plink2 output
-mysumstats = gl.Sumstats("t2d_bbj.txt.gz", fmt="plink2")
+mysumstats = gl.Sumstats("sumstats.txt.gz", fmt="plink2")
 
-# load sumstats with auto mode (auto-detecting common headers) 
+# or load sumstats with auto mode (auto-detecting commonly used headers) 
 # assuming ALT/A1 is EA, and frq is EAF
-mysumstats = gl.Sumstats("t2d_bbj.txt.gz", fmt="auto")
+mysumstats = gl.Sumstats("sumstats.txt.gz", fmt="auto")
 
 # or you can specify the columns:
-mysumstats = gl.Sumstats("t2d_bbj.txt.gz",
+mysumstats = gl.Sumstats("sumstats.txt.gz",
              snpid="SNP",
              chrom="CHR",
              pos="POS",
              ea="ALT",
              nea="REF",
-             neaf="Frq",
+             eaf="Frq",
              beta="BETA",
              se="SE",
              p="P",
@@ -83,26 +105,9 @@ mysumstats.plot_mqq()
 ...
 ```
 
-### install in conda environment
-
-Create a Python 3.9 environment and install gwaslab using pip:
-
-```
-conda env create -n gwaslab_test -c conda-forge python=3.9
-conda activate gwaslab
-pip install gwaslab==3.4.45
-```
-
-or create a new environment using yml file [environment_3.4.40.yml](https://github.com/Cloufield/gwaslab/blob/main/environment_3.4.40.yml)
-
-```
-conda env create -n gwaslab -f environment_3.4.40.yml
-```
-
-
-### install using docker
+## Documentation and tutorials
 
-A docker file is available [here](https://github.com/Cloufield/gwaslab/blob/main/docker/Dockerfile) for building local images.
+Documentation and tutorials for GWASLab are avaiable at [here](https://cloufield.github.io/gwaslab/).
 
 ## Functions
 
@@ -149,7 +154,7 @@ A docker file is available [here](https://github.com/Cloufield/gwaslab/blob/main
 - Scatter plot: allele frequency comparison 
 - Scatter plot: trumpet plot (plot of MAF and effect size with power lines)
 
-### Visualization Examples
+#### Visualization Examples
 
 <img width="600" alt="image" src="https://user-images.githubusercontent.com/40289485/233836639-34b03c47-5a59-4fd4-9677-5e13b02aab15.png">
 <img width="600" alt="image" src="https://user-images.githubusercontent.com/40289485/197393168-e3e7076f-2801-4d66-9526-80778d44f3da.png">
@@ -165,42 +170,15 @@ A docker file is available [here](https://github.com/Cloufield/gwaslab/blob/main
 - Sumstats summary: give you a quick overview of the sumstats. 
 - ...
 
-## Requirements (deprecated)
-
-environment.yml
+## Issues
 
-```
-name: gwaslab
-channels:
-  - conda-forge
-  - defaults
-dependencies:
-  - python=3.8.16=h7a1cb2a_3
-  - jupyter==1.0.0
-  - pip==23.1.2
-  - pip:
-      - adjusttext==0.8
-      - biopython==1.81
-      - gwaslab==3.4.16
-      - liftover==1.1.16
-      - matplotlib==3.7.1
-      - numpy==1.24.2
-      - pandas==1.4.4
-      - scikit-allel==1.3.5
-      - scikit-learn==1.2.2
-      - scipy==1.10.1
-      - seaborn==0.11.2
-      - statsmodels==0.13
-      - adjustText==0.8
-      - pysam==0.19
-      - pyensembl==2.2.3
-      - h5py==3.10.0
-```
+- GWASLab is currently under active development, with frequent updates.
+- Note: Known issues are documented at https://cloufield.github.io/gwaslab/KnownIssues/.
 
 ## How to cite
 - GWASLab preprint: He, Y., Koido, M., Shimmori, Y., Kamatani, Y. (2023). GWASLab: a Python package for processing and visualizing GWAS summary statistics. Preprint at Jxiv, 2023-5. https://doi.org/10.51094/jxiv.370
 
-## Sample Data
+## Sample data used for tutorial
 - Sample GWAS data used in GWASLab is obtained from: http://jenger.riken.jp/ (Suzuki, Ken, et al. "Identification of 28 new susceptibility loci for type 2 diabetes in the Japanese population." Nature genetics 51.3 (2019): 379-386.).
 
 ## Acknowledgement

{gwaslab-3.5.7 → gwaslab-3.6.0}/README.md

@@ -1,48 +1,69 @@
 # GWASLab
 
-<img width="600" alt="image" src="https://user-images.githubusercontent.com/40289485/197167760-5f761f5e-5856-4b27-a540-8b9cd90bdadb.png">
+<img width="600" alt="image" src="https://github.com/user-attachments/assets/109262c6-c870-4078-94b5-66cf8c6b13c4" />
 
 ![badge](https://img.shields.io/pypi/v/gwaslab)
 [![Downloads](https://static.pepy.tech/badge/gwaslab)](https://pepy.tech/project/gwaslab)
 ![badge_pip](https://img.shields.io/pypi/dm/gwaslab)
-[![Hits](https://hits.seeyoufarm.com/api/count/incr/badge.svg?url=https%3A%2F%2Fcloufield.github.io%2Fgwaslab%2F&count_bg=%2379C83D&title_bg=%23555555&icon=&icon_color=%23E7E7E7&title=hits&edge_flat=false)](https://hits.seeyoufarm.com)
 ![badge_commit_m](https://img.shields.io/github/commit-activity/m/Cloufield/gwaslab)
 
-* A handy Python toolkit for handling GWAS summary statistics (sumstats).
+* A handy Python-based toolkit for handling GWAS summary statistics (sumstats).
 * Each process is modularized and can be customized to your needs.
 * Sumstats-specific manipulations are designed as methods of a Python object, `gwaslab.Sumstats`.
 
-Please check GWASLab documentation at [https://cloufield.github.io/gwaslab/](https://cloufield.github.io/gwaslab/)
+## Installation
 
-Note: GWASLab is being updated very frequently for now. I will release the first stable version soon! Please stay tuned.
+### install via pip
 
-Warning: Known issues of GWASLab are summarized in [https://cloufield.github.io/gwaslab/KnownIssues/](https://cloufield.github.io/gwaslab/KnownIssues/) .
+The latest version of GWASLab now supports Python 3.9, 3.10, 3.11, and 3.12.
 
-## Install
+```bash
+pip install gwaslab
+```
 
-### install via pip
+### install in conda environment
+
+Create a Python 3.9, 3.10, 3.11 or 3.12 environment and install gwaslab using pip:
+
+```bash
+conda env create -n gwaslab -c conda-forge python=3.12
+
+conda activate gwaslab
 
+pip install gwaslab
 ```
-pip install gwaslab==3.5.4
+
+or create a new environment using yml file [environment.yml](https://github.com/Cloufield/gwaslab/blob/main/environment.yml)
+
+```bash
+conda env create -n gwaslab -f environment.yml
 ```
 
+### install using docker (deprecated)
+
+A docker file is available [here](https://github.com/Cloufield/gwaslab/blob/main/docker/Dockerfile) for building local images.
+
+## Quick start
+
 ```python
+
 import gwaslab as gl
+
 # load plink2 output
-mysumstats = gl.Sumstats("t2d_bbj.txt.gz", fmt="plink2")
+mysumstats = gl.Sumstats("sumstats.txt.gz", fmt="plink2")
 
-# load sumstats with auto mode (auto-detecting common headers) 
+# or load sumstats with auto mode (auto-detecting commonly used headers) 
 # assuming ALT/A1 is EA, and frq is EAF
-mysumstats = gl.Sumstats("t2d_bbj.txt.gz", fmt="auto")
+mysumstats = gl.Sumstats("sumstats.txt.gz", fmt="auto")
 
 # or you can specify the columns:
-mysumstats = gl.Sumstats("t2d_bbj.txt.gz",
+mysumstats = gl.Sumstats("sumstats.txt.gz",
              snpid="SNP",
              chrom="CHR",
              pos="POS",
              ea="ALT",
              nea="REF",
-             neaf="Frq",
+             eaf="Frq",
              beta="BETA",
              se="SE",
              p="P",
@@ -55,26 +76,9 @@ mysumstats.plot_mqq()
 ...
 ```
 
-### install in conda environment
-
-Create a Python 3.9 environment and install gwaslab using pip:
-
-```
-conda env create -n gwaslab_test -c conda-forge python=3.9
-conda activate gwaslab
-pip install gwaslab==3.4.45
-```
-
-or create a new environment using yml file [environment_3.4.40.yml](https://github.com/Cloufield/gwaslab/blob/main/environment_3.4.40.yml)
-
-```
-conda env create -n gwaslab -f environment_3.4.40.yml
-```
-
-
-### install using docker
+## Documentation and tutorials
 
-A docker file is available [here](https://github.com/Cloufield/gwaslab/blob/main/docker/Dockerfile) for building local images.
+Documentation and tutorials for GWASLab are avaiable at [here](https://cloufield.github.io/gwaslab/).
 
 ## Functions
 
@@ -121,7 +125,7 @@ A docker file is available [here](https://github.com/Cloufield/gwaslab/blob/main
 - Scatter plot: allele frequency comparison 
 - Scatter plot: trumpet plot (plot of MAF and effect size with power lines)
 
-### Visualization Examples
+#### Visualization Examples
 
 <img width="600" alt="image" src="https://user-images.githubusercontent.com/40289485/233836639-34b03c47-5a59-4fd4-9677-5e13b02aab15.png">
 <img width="600" alt="image" src="https://user-images.githubusercontent.com/40289485/197393168-e3e7076f-2801-4d66-9526-80778d44f3da.png">
@@ -137,42 +141,15 @@ A docker file is available [here](https://github.com/Cloufield/gwaslab/blob/main
 - Sumstats summary: give you a quick overview of the sumstats. 
 - ...
 
-## Requirements (deprecated)
-
-environment.yml
+## Issues
 
-```
-name: gwaslab
-channels:
-  - conda-forge
-  - defaults
-dependencies:
-  - python=3.8.16=h7a1cb2a_3
-  - jupyter==1.0.0
-  - pip==23.1.2
-  - pip:
-      - adjusttext==0.8
-      - biopython==1.81
-      - gwaslab==3.4.16
-      - liftover==1.1.16
-      - matplotlib==3.7.1
-      - numpy==1.24.2
-      - pandas==1.4.4
-      - scikit-allel==1.3.5
-      - scikit-learn==1.2.2
-      - scipy==1.10.1
-      - seaborn==0.11.2
-      - statsmodels==0.13
-      - adjustText==0.8
-      - pysam==0.19
-      - pyensembl==2.2.3
-      - h5py==3.10.0
-```
+- GWASLab is currently under active development, with frequent updates.
+- Note: Known issues are documented at https://cloufield.github.io/gwaslab/KnownIssues/.
 
 ## How to cite
 - GWASLab preprint: He, Y., Koido, M., Shimmori, Y., Kamatani, Y. (2023). GWASLab: a Python package for processing and visualizing GWAS summary statistics. Preprint at Jxiv, 2023-5. https://doi.org/10.51094/jxiv.370
 
-## Sample Data
+## Sample data used for tutorial
 - Sample GWAS data used in GWASLab is obtained from: http://jenger.riken.jp/ (Suzuki, Ken, et al. "Identification of 28 new susceptibility loci for type 2 diabetes in the Japanese population." Nature genetics 51.3 (2019): 379-386.).
 
 ## Acknowledgement

{gwaslab-3.5.7 → gwaslab-3.6.0}/pyproject.toml

@@ -7,7 +7,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "gwaslab"
-version = "3.5.7"
+version = "3.6.0"
 authors = [
   { name="Yunye", email="yunye@gwaslab.com" },
 ]
@@ -34,7 +34,7 @@ dependencies = [
 requires-python = ">=3.9,<3.13"
 classifiers = [
     "Programming Language :: Python :: 3",
-    "License :: OSI Approved :: MIT License",
+    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
     "Operating System :: OS Independent",
 ]
 

{gwaslab-3.5.7 → gwaslab-3.6.0}/src/gwaslab/__init__.py

@@ -1,6 +1,8 @@
 from gwaslab.g_Sumstats import Sumstats
+from gwaslab.g_Sumstats_polars import Sumstatsp
 from gwaslab.g_SumstatsT import SumstatsT
 from gwaslab.g_SumstatsPair import SumstatsPair
+from gwaslab.g_SumstatsMulti import SumstatsMulti
 from gwaslab.util_in_convert_h2 import h2_obs_to_liab
 from gwaslab.util_in_convert_h2 import _get_per_snp_r2
 from gwaslab.util_in_convert_h2 import h2_se_to_p

{gwaslab-3.5.7 → gwaslab-3.6.0}/src/gwaslab/bd_common_data.py

@@ -337,6 +337,7 @@ def _maketrans(complement_mapping):
     """
     keys = "".join(complement_mapping.keys()).encode("ASCII")
     values = "".join(complement_mapping.values()).encode("ASCII")
+
     return bytes.maketrans(keys + keys.lower(), values + values.lower())
         
 ####################################################################################################################   

{gwaslab-3.5.7 → gwaslab-3.6.0}/src/gwaslab/bd_get_hapmap3.py

@@ -43,7 +43,6 @@ def gethapmap3(sumstats,rsid="rsID",chrom="CHR", pos="POS", ea="EA", nea="NEA",b
     else:
         additional_cols=[]
     hapmap3_ref = pd.read_csv(data_path,sep="\s+",usecols=["#CHROM","POS","rsid"]+additional_cols, dtype={"#CHROM":"string","POS":"string"})
-
     #rsid    A1      A2      #CHROM  POS
     #rs3094315       G       A       1       752566
     

{gwaslab-3.5.7 → gwaslab-3.6.0}/src/gwaslab/data/formatbook.json

@@ -237,6 +237,16 @@
             "TotalSampleSize": "N",
             "Nsample": "N",
             "num_samples": "N",
+            "Neff": "N_EFF",
+            "N_EFF": "N_EFF",
+            "N_CASE": "N_CASE",
+            "Ncase": "N_CASE",
+            "ncase": "N_CASE",
+            "n_case": "N_CASE",
+            "Ncontrol": "N_CONTROL",
+            "N_control": "N_CONTROL",
+            "N_Control": "N_CONTROL",
+            "NCONTROL": "N_CONTROL",
             "beta": "BETA",
             "BETA": "BETA",
             "Beta": "BETA",
@@ -461,6 +471,31 @@
             "Direction": "DIRECTION"
         }
     },
+    "genomicsem": {
+        "meta_data": {
+            "format_name": "genomicSEM",
+            "format_source": "https://github.com/GenomicSEM/GenomicSEM/wiki/4.-Common-Factor-GWAS",
+            "format_source2": "https://github.com/GenomicSEM/GenomicSEM/wiki/5.-Multivariate-GWAS",
+            "format_version": 20241210
+        },
+        "format_dict": {
+            "SNP": "rsID",
+            "A2": "NEA",
+            "A1": "EA",
+            "Frq": "EAF",
+            "MAF": "MAF",
+            "N": "N",
+            "est": "BETA",
+            "se_c": "SE",
+            "Pval_Estimate": "P",
+            "Z_Estimate": "Z",
+            "Q": "Q",
+            "Q_df": "DOF",
+            "Q_pval": "P_HET",
+            "CHR": "CHR",
+            "BP": "POS"
+        }
+    },
     "plink_fam": {
         "meta_data": {
             "format_name": "plink_fam",
@@ -880,6 +915,21 @@
             "POS": "POS"
         }
     },
+    "mesusie": {
+        "meta_data": {
+            "format_name": "MESuSiE",
+            "format_source": "https://borangao.github.io/meSuSie_Analysis/installation.html",
+            "format_version": 20221109
+        },
+        "format_dict": {
+            "SNP": "SNPID",
+            "N": "N",
+            "Beta": "BETA",
+            "Se": "SE",
+            "Z": "Z",
+            "POS": "POS"
+        }
+    },
     "plink2_linear": {
         "meta_data": {
             "format_name": "PLINK2 .glm.linear",
@@ -1032,6 +1082,34 @@
             "ci_upper": "OR_95U"
         }
     },
+    "ccgwas": {
+        "meta_data": {
+            "format_name": "CCGWAS",
+            "format_source": "https://github.com/wouterpeyrot/CCGWAS",
+            "format_version": "20220901",
+            "last_check_date": "20250416",
+            "format_separator": "\t",
+            "format_citation": "Peyrot, W. J., & Price, A. L. (2021). Identifying loci with different allele frequencies among cases of eight psychiatric disorders using CC-GWAS. Nature genetics, 53(4), 445-454.",
+            "format_comment": null,
+            "format_na": null,
+            "format_other_cols": [
+                "Exact_beta",
+                "Exact_se",
+                "Exact_pval",
+                "CCGWAS_signif"
+            ]
+        },
+        "format_dict": {
+            "SNP": "SNPID",
+            "CHR": "CHR",
+            "BP": "POS",
+            "A2": "NEA",
+            "A1": "EA",
+            "OLS_beta": "BETA",
+            "OLS_se": "SE",
+            "OLS_pval": "P"
+        }
+    },
     "fastgwa": {
         "meta_data": {
             "format_name": "fastgwa",

{gwaslab-3.5.7 → gwaslab-3.6.0}/src/gwaslab/data/reference.json

@@ -103,7 +103,9 @@
     "13to19":"https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/chain/v1_nflo/chm13v2-hg19.chain",
     "13to38":"https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/chain/v1_nflo/chm13v2-grch38.chain",
     "18to19":"https://hgdownload.soe.ucsc.edu/goldenPath/hg18/liftOver/hg18ToHg19.over.chain.gz",
-    "18to38":"https://hgdownload.soe.ucsc.edu/goldenPath/hg18/liftOver/hg18ToHg38.over.chain.gz"
+    "18to38":"https://hgdownload.soe.ucsc.edu/goldenPath/hg18/liftOver/hg18ToHg38.over.chain.gz",
+    "1kg_hm3_hg38_eaf":"https://www.dropbox.com/scl/fi/ymkqfsaec6mwjzlvxsm45/PAN.hapmap3.hg38.EAF.tsv.gz?rlkey=p1auef5y1kk7ui41k6j3s8b0z&dl=1",
+    "1kg_hm3_hg19_eaf":"https://www.dropbox.com/scl/fi/dmv9wtfchv6ahim86d49r/PAN.hapmap3.hg19.EAF.tsv.gz?rlkey=ywne2gj1rlm2nj42q9lt2d99n&dl=1"
 }