semvec/pypi-packages huggingface dataset:
thinclient 0.0.1
A thinclient for the Katzenpost client daemon
Requires Python: >=3.8


# thin client library for Katzenpost client daemon

A thin client library is designed to talk to the katzenpost mixnet client daemon.
It's kind of like a dumb terminal, it doesn't know how to do much besides
message passing. All the hard work is done by the client daemon.

Here's our thin client integration guide:
https://github.com/katzenpost/website/blob/main/content/en/docs/client_integration.md

Here's the client2 daemon source code:
https://github.com/katzenpost/katzenpost/tree/main/client2

That directory has a Makefile which will give you two ways to build the daemon:

1. Makefile target "warpedclientdaemon": build binary for use with docker test mixnet.
2. Makefile target "clientdaemon": build binary for production mixnet.

We recommend that you look over the client2.toml configuration file generated by
our dockerized test mixnet. Using that configuration file you can either make
the daemon listen for thin client connections on a TCP/IP socket or you can
specify a UNIX domain socket.

### Compatibility

This git repo contains two implementations of the thin client for katzenpost mixnet.
One of them is written in Python and the other is written in Rust. Both use async io.

Works with Katzenpost v0.0.40 or later.


## Rust

**thin client library for Rust**

*This thin client has full feature parity with the golang reference thin client.*

**compile rust crate as usual**

```bash
cargo build

```


## Python

**thin client library for Python**

Currently the python implementation only supports using UNIX domain sockets.

**install**

```bash
pip instal -e .
```


# License

AGPLv3
nanoCEM 0.0.6.3
A simple tool designed to visualize the features that distinguish between two groups of ONT data at the site level.                It supports 4 re-squiggle program(tombo resquiggle/f5c resquiggle/f5c eventalign/move_table).
Requires Python: <=3.11.7,>=3.7.0

# nanoCEM ![logo](docs/logo_tiny.png "nanoCEM")
<a href="https://pypi.python.org/pypi/nanoCEM" rel="pypi">![PyPI](https://img.shields.io/pypi/v/nanoCEM?color=green) </a>
<a href="https://opensource.org/license/mit/" rel="license">![License](https://img.shields.io/pypi/l/nanoCEM?color=orange)</a>

The nanopore current events magnifier (`nanoCEM`) is a python command line to facilitate the analysis of DNA/RNA modification sites by visualizing statistical features of current events. 
NanoCEM can be used to showcase high confidence sites and observe the difference based on the modification sample and the low or no modification sample.

It supports two re-squiggle pipeline(`Tombo` and `f5c`) and support `R9` and `R10`.
If you want to view single read signal or raw signal, [Squigualiser](https://github.com/hiruna72/squigualiser) is recommended.

## Installation

Before pip install, make sure you have installed the `samtools`(>=1.16) , `f5c`(>=1.4), `slow5tools`(>=1.1.0) and `minimap2`(>=2.17),

    conda install samtools=1.16 minimap2 f5c=1.4 slow5tools -c conda-forge -c bioconda 

To install the latest nanoCEM

    pip install nanoCEM

And install from the resource

    git clone https://github.com/lrslab/nanoCEM.git
    cd nanoCEM/
    pip install .
To install nanoCEM from docker,

    docker pull zhihaguo/nanocem_env
    
To check the version of nanoCEM, run:

    pip list | grep nanoCEM


## Solutions for some potential environment problem
Although it does not affect the functionality, the issue of possible missing header files caused by **samtools** installation by conda can be resolved with the following command.

    conda install -c conda-forge ncurses

The potential **vbz** format compression issue when reading **fast5** files.

    conda install -c bioconda ont_vbz_hdf_plugin



## Data release
For the data we used and related commands in our paper, please view our [wiki](https://github.com/lrslab/nanoCEM/wiki/Data-release-and-commands)

## Documents
Full documentation is available at https://nanocem.readthedocs.io/

## Publication
Our paper is online [here](https://academic.oup.com/nargab/article/6/2/lqae052/7676831) now

## Workflow
![workflow](docs/Workflow.png)