semvec/pypi-packages huggingface dataset:
nanoepiseg 1.0.0b3
Methylome segmentation algorithm using a changepoint detection HMM
License: MIT
Requires Python: >=3.7

# NanoEpiSeg 1.0.0b3

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NanoEpiSeg is a tool for *de novo* segmentation of  a methylome from read-level methylation calls (such as Nanopolish).

NanoEpiSeg is currently in development. Please do not hesitate to report bugs or feature requests.

A detailed documentation is in the works, stay tuned!
## Prerequisites

NanoEpiSeg assumes that your methylation calls are stored in [MetH5](http://github.com/snajder-r/meth5format) format.

## Installation

Through pip:

```
pip install nanoepiseg
````

Through anaconda:

```
conda install -c snajder-r nanoepiseg
```

## Usage

NanoEpiSeg is meant to be parallelizable, which is why you would typically call nanoepiseg on a cluster system in parallel.
In order to best accomplish load-balancing, it is done per hdf5 chunk. 

You can list the number of chunks per chromosome via:

```bash
nanoepiseg list_chunks --m5file INPUT_FILE.m5
```

To then perform segmentation for a certain chunk, you can run:

```bash
nanoepiseg segment_h5 --m5file INPUT_FILE.m5 \
    --out_tsv OUTPUT_FILE \ 
    --reader_workers NUM_READER_WORKERS \ 
    --workers NUM_SEGMENTATION_WORKERS \ 
    --chromosome CHROMOSOME \
    --chunks CHUNK1 [CHUNK2 ...]
```

There are further options available. Please check out the help to discover them.
pyls-flake8 0.4.0
A Flake8 plugin for the Python Language Server
License: MIT

# pyls-flake8

A Flake8 plugin for the
[Python LSP Server](https://github.com/python-lsp/python-lsp-server).

Install this plugin in the same environment as `python-lsp-server`:

```shell
pip install pyls-flake8
```

pyls-flake8 will read its config from your project's ``setup.cfg``,
``tox.ini`` or ``.flake8`` file if it has one.