semvec/pypi-packages huggingface dataset:
cojopy 0.1.2
Conditional Analysis with LD Matrix.
License: MIT
Requires Python: <3.13,>=3.9

# cojopy


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Conditional Analysis with LD Matrix

Get the same results as [GCTA COJO](https://yanglab.westlake.edu.cn/software/gcta/#COJO), but with LD matrix.

## Installation

```bash
pip install cojopy
```

## Usage

### Input files
#### Summary statistics file

The summary statistics file should have the following columns (same as the cojo file of GCTA):

- SNP: SNP ID
- A1: Effect allele
- A2: Other allele
- b: Effect size
- se: Standard error
- p: P-value
- freq: Minor allele frequency
- N: Sample size


#### LD matrix file
- A tab-delimited LD matrix, same as the output of `plink --r square`.
> [!Note]
> The allele order of the summary statistics file should be the same as the allele order of the LD matrix file.


### Stepwise model selection of independent associated SNPs (same as `gcta --cojo-slct`)

```bash
cojo slct \
--sumstats ./exampledata/sim_gwas.ma \
--ld-matrix ./exampledata/sim_r.ld \
--output ./exampledata/slct.txt
```

### Fit all the included SNPs to estimate their joint effects without model selection (same as `gcta --cojo-joint`)

```bash
cojo joint \
--sumstats ./exampledata/sim_gwas.ma \
--ld-matrix ./exampledata/sim_r.ld \
--extract-snps ./exampledata/extract_snps.txt \
--output ./exampledata/joint.txt
```

### Perform association analysis of the included SNPs conditional on the given list of SNPs (same as `gcta --cojo-cond`)

```bash
cojo cond \
--sumstats ./exampledata/sim_gwas.ma \
--ld-matrix ./exampledata/sim_r.ld \
--cond-snps ./exampledata/cond_snps.txt \
--output ./exampledata/cond.txt
```

### Parameters

- `cond-snps`: For `cond` command, path to the file containing the SNPs to condition on, one SNP per line.
- `extract-snps`: For `joint` and `cond` commands, path to the file containing the SNPs to extract, one SNP per line.
- `ld-freq`: Path to the LD frequency file, optional, use freq in sumstats if not provided.
- `p-cutoff`: P-value cutoff, default is 5e-8.
- `collinear-cutoff`: Collinearity cutoff, default is 0.9.
- `maf-cutoff`: Minor allele frequency cutoff, default is 0.01.
- `diff-freq-cutoff`: Difference in minor allele frequency cutoff, default is 0.2, won't take effect unless `ld-freq` is provided.
codeowners 0.8.0
Codeowners parser for Python
License: MIT
Requires Python: <4.0,>=3.7
Keywords: codeowners, git, github

# codeowners [![CircleCI](https://circleci.com/gh/sbdchd/codeowners.svg?style=svg)](https://circleci.com/gh/sbdchd/codeowners) [![pypi](https://img.shields.io/pypi/v/codeowners.svg)](https://pypi.org/project/codeowners/)

> Python codeowners parser based on [softprops's Rust
> library](https://crates.io/crates/codeowners) and [hmarr's Go
> library](https://github.com/hmarr/codeowners/).

## Why?

To allow Python users to parse [codeowners
files](https://docs.github.com/en/github/creating-cloning-and-archiving-repositories/about-code-owners#codeowners-syntax)
in Python.

## Install

```shell
pip install codeowners
```

## Usage

```python
from codeowners import CodeOwners

example_file = """\
# owners for js files
*.js    @ghost
# python
*.py user@example.com
# misc
/build/logs/ @dmin
docs/*  docs@example.com
"""

owners = CodeOwners(example_file)
assert owners.of("test.js") ==  [('USERNAME', '@ghost')]
```

## Dev

```shell
poetry install

s/test

s/lint
```

## Releasing a New Version

```shell
# bump version in pyproject.toml

# update CHANGELOG.md

# commit release commit to GitHub

# build and publish
poetry publish --build

# create a release in the GitHub UI
```
xtnote 0.1.0
A simple command-line note-taking tool
License: MIT
Requires Python: >=3.6

# xtnote - Simple CLI Note Manager

`xtnote` is a command-line tool for managing your notes and topics directly from your terminal. It stores notes as plain Markdown files in a dedicated directory (`~/.Note`) and provides an interactive menu for common note-taking tasks.

## Features

* **Interactive Menu:** Navigate common actions using arrow keys.
* **Note Creation:** Create new Markdown notes (`.md`) in the root of your notes directory or within topics.
* **Topic (Folder) Creation:** Organize your notes by creating topics. Supports nested topics.
* **Nested Structure:** Create notes and topics inside existing topics to build a hierarchical structure.
* **List Items:** View a structured list of all your notes and topics.
* **Open Items:** Select a note to open it in your preferred command-line editor (like `nvim`, `vim`, `nano`, etc.). You can also open the entire `~/.Note` directory in your editor.
* **Delete Items:** Safely delete notes or topics (with confirmation).
* **Configurable Editor:** Uses the `EDITOR` environment variable, falling back to `nvim` if not set.

## Installation

You can install `xtnote` using pip:

```bash
pip install xtnote