semvec/pypi-packages huggingface dataset:
methdb 0.0.2
mdb: population-level DNA methylation analysis toolkit
License: MIT
Requires Python: >=3.10

# mdb
A toolkit to create DNA methylation database for cross-sample comparison 


## Requirement
**Output format taken from:**
- Modkit >= v0.6
- Pb-CpG-tools >= v3.0.0

**Recommended DNA methylation pileup parameter:**
- Use `--combine-strand` in modkit pileup. 
- Use `-m` function to aggregrate 5mC and 5hmC for ONT's pileup if merging ONT with PacBio.

**mdb features**
- mdb creates a genome-wide CpG matrix to support massive computing with population-level DNA methylation signals
- Use `mdb index` to index reference genome
- Use `mdb create` to create `.mdb` files (a set of `.npy` files) for each methylBED file
- Use `mdb merge` to merge per sample `.mdb` database to form a CpGxSample matrix
- Use `mdb pca` to parform PCA on merged matrix 


        usage: mdb [-h] [-v] {index,create,merge,pca} ...

        DNA methylation database builder for quick population-level analysis.

        positional arguments:
        {index,create,merge,pca}
            index               Index all CpG locations on the reference genome
            create              Create single sample-level methylation database
            merge               mdb databases from multiple samples into a single database: COMBINE STRAND and HAPLOTYPE
            pca                 Perform PCA on the merged mdb database

        options:
        -h, --help            show this help message and exit
        -v, --version         show program's version number and exit

        Version v0.0.2
uptime-kuma-api-v2 1.0.1
A python wrapper for the Uptime Kuma WebSocket API
License: MIT
Requires Python: <4,>=3.7

# uptime-kuma-api-v2

A wrapper for the Uptime Kuma Socket.IO API
---
uptime-kuma-api-v2 is a Python wrapper for the [Uptime Kuma](https://github.com/louislam/uptime-kuma) Socket.IO API.

Based on Original Version by https://github.com/lucasheld/uptime-kuma-api


Python version 3.7+ is required.

Supported Uptime Kuma versions:

| Uptime Kuma     | uptime-kuma-api-v2 |
|-----------------|-----------------|
| 2.0.0-beta.2     | 1.0.0 - 1.0.1   |


Installation
---
uptime-kuma-api-v2 is available on the [Python Package Index (PyPI)](https://pypi.org/project/uptime-kuma-api-v2/).

You can install it using pip:

```
pip install uptime-kuma-api-v2
```

Documentation
---
The API Reference is available on [Read the Docs](https://uptime-kuma-api-v2.readthedocs.io).

Example
---
Once you have installed the python package, you can use it to communicate with an Uptime Kuma instance.

To do so, import `UptimeKumaApi` from the library and specify the Uptime Kuma server url (e.g. 'http://127.0.0.1:3001'), username and password to initialize the connection.

```python
>>> from uptime_kuma_api import UptimeKumaApi, MonitorType
>>> api = UptimeKumaApi('INSERT_URL')
>>> api.login('INSERT_USERNAME', 'INSERT_PASSWORD')
```

Now you can call one of the existing methods of the instance. For example create a new monitor:

```python
>>> result = api.add_monitor(type=MonitorType.HTTP, name="Google", url="https://google.com")
>>> print(result)
{'msg': 'Added Successfully.', 'monitorId': 1}
```

At the end, the connection to the API must be disconnected so that the program does not block.

```python
>>> api.disconnect()
```

With a context manager, the disconnect method is called automatically:

```python
from uptime_kuma_api import UptimeKumaApi

with UptimeKumaApi('INSERT_URL') as api:
    api.login('INSERT_USERNAME', 'INSERT_PASSWORD')
    api.add_monitor(
        type=MonitorType.HTTP,
        name="Google",
        url="https://google.com"
    )
```