semvec/pypi-packages huggingface dataset:
tssenrich 1.4.6
Calculate TSS enrichment for ATAC-seq data

# tssenrich

Calculate [TSS enrichment](https://www.encodeproject.org/data-standards/terms/#enrichment) for ATAC-seq data. (see also the [ENCODE standards](https://www.encodeproject.org/atac-seq/))

## Installation
```
pip install tssenrich
```
or
```
pip install --user tssenrich
```

## Usage
```
usage: tssenrich [-h] [--genome {hg38,hg19,mm10,</path/to/file.bed.gz>}] [--names] [--memory <float>] [--processes <int>]
                 [--mapping-quality <int>] [--samtools-path <path/to/samtools>] [--log <path/to/log.txt>]
                 [--tmp-dir <temp/file/dir/>] [--flank-distance <int>] [--flank-size <int>]
                 <path/to/file.bam> [<path/to/file.bam> ...]

calculate TSS enrichment for ATAC-seq data

positional arguments:
  <path/to/file.bam>    Path to input BAM file

optional arguments:
  -h, --help            show this help message and exit
  --genome {hg38,hg19,mm10,</path/to/file.bed.gz>}
                        genome build or path to BED file [hg38]
  --names               include sample names in output
  --memory <float>      memory limit in GB [2]
  --processes <int>     number of processes/threads to use [1]
  --mapping-quality <int>
                        ignore reads with mapping quality below the given value [0]
  --samtools-path <path/to/samtools>
                        path to an alternate samtools executable [/opt/anaconda3/envs/tssenrich/bin/samtools]
  --log <path/to/log.txt>
                        path to log file
  --tmp-dir <temp/file/dir/>
                        directory to use for temporary files
  --flank-distance <int>
                        distance from tss of outer ends of flanks [1000]
  --flank-size <int>    size of flanks (for determining average depth) [100]

ENCODE standards:
| Genome | Concerning | Acceptable | Ideal |
| ------ | ---------- | ---------- | ----- |
| hg19   | < 6        | 6 - 10     | > 10  |
| hg38   | < 5        | 5 - 7      | > 7   |
| mm10   | < 10       | 10 - 15    | > 15  |
```

## Examples
```sh
tssenrich example.bam > score.txt
```

```sh
tssenrich --genome hg19 --log log.txt --memory 2 --processes 2 example1.bam example2.bam > scores.txt
```
wasp-map 0.3.5
Utilites for the mapping pipeline from WASP

# wasp_map
Utilites for the mapping pipeline from [WASP](https://github.com/bmvdgeijn/WASP)

## Installation

**Step 0 (optional):** If you wish to specify the locations of the Anaconda3
and/or WASP installations, you can do so through the environment variables
`WASP_MAP_ANACONDA_DIR` and `WASP_MAP_DIR`. For example, you could append this
to your `.bash_profile`:
```sh
export WASP_MAP_ANACONDA_DIR=~/anaconda3
export WASP_MAP_DIR=~/WASP
```

If these environment variables point to already-existing installations of
Anaconda3 and WASP, respectively, then you can skip step 2 (running
`wasp_map-download`).

If you also set environment variable `LD_LIBRARY_PATH` appropriately, you can
skip step 3 (running `wasp_map-set-ldlib`). For example:

```sh
export WASP_MAP_ANACONDA_DIR=~/anaconda3
export WASP_MAP_DIR=~/WASP
export LD_LIBRARY_PATH=${WASP_MAP_ANACONDA_DIR}/lib:$LD_LIBRARY_PATH
```

**Step 1:** install the python package via `pip3`:
```sh
pip3 install wasp_map
```
or
```sh
pip3 install --user wasp_map
```

**Step 2:** Once the python package is installed, run
```sh
wasp_map-download
```
and follow the prompts. Anaconda3 and/or WASP will be installed, if necessary.

**Step 3:** Next, run
```sh
wasp_map-set-ldlib
```
and follow the instruction. It will be something like:
```
Run the following `export` command, or append it to your .bashrc, .profile, or .bash_profile:
export LD_LIBRARY_PATH=/home/aaylward/.local/lib/python3.6/site-packages/wasp_map/anaconda3/lib:$LD_LIBRARY_PATH
```
accelasc 1.0.4
implementation of accel_asc algorithm for integer partitions

# accelasc

Implementation of the `accel_asc` algorithm for integer partitions. See
[this stackoverflow post](https://stackoverflow.com/questions/10035752/elegant-python-code-for-integer-partitioning)
and [Jerome Kelleher's website](http://jeromekelleher.net/category/combinatorics.html).
See also the paper by Kelleher and O'Sullivan: [Generating All Partitions: A Comparison Of Two Encodings](https://arxiv.org/abs/0909.2331).

## Installation
```sh
pip3 install accelasc
```
or
```sh
pip3 install --user accelasc
```

## Usage

```python3
from accelasc import accel_asc
tuple(accel_asc(5))
```
```python3
([1, 1, 1, 1, 1], [1, 1, 1, 2], [1, 1, 3], [1, 2, 2], [1, 4], [2, 3], [5])
```
bagpy 0.5
A python class to facilitate the reading of rosbag file based on semantic datatypes.
Keywords: Autonomous vehicle,ACC,adaptive cruise control,ROS,Robotics

<img src="https://raw.githubusercontent.com/jmscslgroup/bagpy/master/banner_bagpy.png" alt="Strym Logo" align="center"/>

[![Build Status](https://travis-ci.com/jmscslgroup/bagpy.svg?branch=master)](https://travis-ci.com/jmscslgroup/bagpy)
[![Maintenance](https://img.shields.io/badge/Maintained%3F-yes-green.svg)](https://GitHub.com/jmscslgroup/bagpy/graphs/commit-activity)
[![made-with-python](https://img.shields.io/badge/Made%20with-Python-1f425f.svg)](https://www.python.org/)
[![made-with-sphinx-doc](https://img.shields.io/badge/Made%20with-Sphinx-1f425f.svg)](https://www.sphinx-doc.org/)
[![PyPI version shields.io](https://img.shields.io/pypi/v/bagpy.svg)](https://pypi.python.org/pypi/bagpy/)
[![PyPI license](https://img.shields.io/pypi/l/bagpy.svg)](https://pypi.python.org/pypi/bagpy/)
[![Downloads](https://pepy.tech/badge/bagpy)](https://pepy.tech/project/bagpy)



# bagpy
__A Python package to facilitate the reading of a rosbag file based on semantic datatypes.__

__`bagpy`__ provides a wrapper class `bagreader` written in python that provides an easy to use interface for reading 
[bag files](http://wiki.ros.org/Bags) recorded by `rosbag record` command. This wrapper class uses ROS's python API `rosbag`
internally to perform all operations. One of the interesting features about using __`bagreader`__ is that a user doesn't 
need to supply [rostopic name](http://wiki.ros.org/rostopic) to extract relevant data. One can extract data based on the 
type of data the user is seeking.

## Requirements
- Ubuntu 18.04 or later
- Python 3.6 or higher. **Now, the preferred version is Python 3.9**. With other versions, there are some dependency issues as how pip works has changed.
- Python 2.x support not available. Python 3.x virtual environment is recommended for pip installation.
- Works with Windows as well, how, I don't provide support for Windows. See my comment on an issue here: https://github.com/jmscslgroup/bagpy/issues/2#issuecomment-710095649
- **Note: it is not compatible with ROS 2.**

## Installation
```
pip install bagpy
```

## Usage principle
The philosophy behind developing this project is to make everything as simple and less confusing as possible. 
As a result, there are not too many options or freedom of usage being provided by __`bagreader`__ class. 
If you need a wide variety of options, users can directly use ROS's `rosbag` python package or 
Robotics System Toolbox APIs provided by MATLAB. However, if you are looking for simplicity, __`bagpy`__ is an
elegant choice.

## Examples
See Notebooks and python scripts at https://github.com/jmscslgroup/bagpy/tree/master/notebook for examples.
getanime 1.2.0
A Python package to download anime from command line
Requires Python: >=3.7


# Project Title

This project is for Japanese Anime lovers to easily download Animes without interuption e.g ads


## Installation

Clone my project from the repo

```bash
  git clone https://github.com/devoply-dev/cmdanime

  cd cmdanime
```
Driver Installation
--------------------

1. open cmd in Administrator mode and copy and paste the following:
```bash
  @"%SystemRoot%\System32\WindowsPowerShell\v1.0\powershell.exe" -NoProfile -InputFormat None -ExecutionPolicy Bypass -Command "[System.Net.ServicePointManager]::SecurityProtocol = 3072; iex ((New-Object System.Net.WebClient).DownloadString('https://community.chocolatey.org/install.ps1'))" && SET "PATH=%PATH%;%ALLUSERSPROFILE%\chocolatey\bin"
```

2. For WindowsPowerShell Installation, open WindowsPowerShell in Administrator mode and paste the following:
```bash
  Set-ExecutionPolicy Bypass -Scope Process -Force; [System.Net.ServicePointManager]::SecurityProtocol = [System.Net.ServicePointManager]::SecurityProtocol -bor 3072; iex ((New-Object System.Net.WebClient).DownloadString('https://community.chocolatey.org/install.ps1'))
```

3. Then you can use these commands to install the drivers:
```bash
  choco install chromedriver
```

## Appendix
How to use the script
----------------

1. just follow the prompts

2. make sure to enter correct info on any prompt

3. read thru the information printed out after any prompt
## Authors

- [@haxsys](https://github.com/devoply-dev)

MIT License

Copyright (c) 2022 Elenasulu Arinze

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
pylingdocs-gui 0.0.2
A rudimentary GUI editor for pylingdocs.
Keywords: pylingdocs,linguistics

# pylingdocs-gui

![License](https://img.shields.io/github/license/fmatter/pylingdocs-gui)
[![Linting](https://img.shields.io/github/workflow/status/fmatter/pylingdocs-gui/lint?label=linting)](https://github.com/fmatter/pylingdocs-gui/actions/workflows/lint.yml)
[![PyPI](https://img.shields.io/pypi/v/pylingdocs-gui.svg)](https://pypi.org/project/pylingdocs-gui)
![Versions](https://img.shields.io/pypi/pyversions/pylingdocs-gui)

A rudimentary GUI editor for pylingdocs.

* Installation: `pip install pylingdocs-gui`
* Usage: run `pylingdocs-gui` in your pylingdocs project

![Screenshot from 2022-09-22 10-13-03](https://user-images.githubusercontent.com/2378389/191810571-90272c83-37e3-408a-b7ee-4983a23cbef0.png)
tempfifo 1.1.4
This module creates temporary named pipes

# tempfifo

This module creates temporary named pipes

## Installation

```sh
pip3 install tempfifo
```
or
```sh
pip3 install --user tempfifo
```

## Example

A `NamedTemporaryFIFO` class is provided and is intended to be used as a
context manager. The filename of the created pipe is accessible as its `name`
attribute. For example:

```python
from tempfifo import NamedTemporaryFIFO
with NamedTemporaryFIFO() as ntf:
    print(ntf.name)
```
cmdanime 1.0.0
A Python package to download anime from command line
Requires Python: >=3.7


# Project Title

This project is for Japanese Anime lovers to easily download Animes without interuption e.g ads


## Installation

Clone my project from the repo

```bash
  git clone https://github.com/devoply-dev/cmdanime

  cd cmdanime
```
Driver Installation
--------------------

1. open cmd in Administrator mode and copy and paste the following:
```bash
  @"%SystemRoot%\System32\WindowsPowerShell\v1.0\powershell.exe" -NoProfile -InputFormat None -ExecutionPolicy Bypass -Command "[System.Net.ServicePointManager]::SecurityProtocol = 3072; iex ((New-Object System.Net.WebClient).DownloadString('https://community.chocolatey.org/install.ps1'))" && SET "PATH=%PATH%;%ALLUSERSPROFILE%\chocolatey\bin"
```

2. For WindowsPowerShell Installation, open WindowsPowerShell in Administrator mode and paste the following:
```bash
  Set-ExecutionPolicy Bypass -Scope Process -Force; [System.Net.ServicePointManager]::SecurityProtocol = [System.Net.ServicePointManager]::SecurityProtocol -bor 3072; iex ((New-Object System.Net.WebClient).DownloadString('https://community.chocolatey.org/install.ps1'))
```

3. Then you can use these commands to install the drivers:
```bash
  choco install chromedriver
```

## Appendix
How to use the script
----------------

1. just follow the prompts

2. make sure to enter correct info on any prompt

3. read thru the information printed out after any prompt
## Authors

- [@haxsys](https://github.com/devoply-dev)

MIT License

Copyright (c) 2022 Elenasulu Arinze

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.