semvec/pypi-packages huggingface dataset:
d2ssect 0.0.9
Calculate d2s scores from short reads
Requires Python: >=3.7

# d2ssect

![conda install test badge](https://github.com/iracooke/d2ssect/actions/workflows/conda.yml/badge.svg)
![linux install test badge](https://github.com/iracooke/d2ssect/actions/workflows/linux.yml/badge.svg)
![macos install test badge](https://github.com/iracooke/d2ssect/actions/workflows/macos.yml/badge.svg)

`d2ssect` calculates an alignment-free distance between samples based on frequencies of shared kmers. Specifically, it provides a fast implementation of the [D2S statistic](https://www.liebertpub.com/doi/10.1089/cmb.2009.0198) which can be used as a standalone distance measure, or as input to a range of methods (eg see [these tools](https://github.com/chanlab-genomics/alignment-free-tools)) for phylogenetic and network analysis.


## Installation

`d2ssect` is available via [pypi](https://pypi.org/project/d2ssect/).  Installation requires python 3.7 or greater as well as the [jellyfish](https://github.com/gmarcais/Jellyfish) program and libraries.  We recommend installation into a conda environment as follows
```bash
conda create -n d2ssect python=3.7 kmer-jellyfish
conda activate d2ssect
pip install d2ssect
d2ssect -h
```

Alternatively, you may use an existing Jellyfish installation, or install Jellyfish without using conda. If using this method please note that;

- Jellyfish version 2 is required (Jellyfish 1 will not work)
- Installation of Jellyfish via linux package managers will not work as this installs the jellyfish binary but not libraries and headers needed by `d2ssect`

Once Jellyfish is installed you should then be able to install `d2ssect` using pip or pip3 as follows
```bash
pip install d2ssect
```


## Usage

Lets say we have a collection of fastq files corresponding to sequencing reads from different samples. We want to compare these with `d2ssect`.  First count kmers in these files using `jellyfish`

```bash
for f in *.fastq;do jellyfish count -m 21 -s 10000000 $f -o ${f%.fastq}.jf ;done
```

Note that the command above will create a corresponding `.jf` file for every `.fastq` file in the current directory. By keeping the base names of the `jf` and `fastq` files identical we can then run `d2ssect` as follows;

```bash
d2ssect -l *.jf -f *.fastq
```

## Outputs

`d2ssect` provides information on progress (sent to stderr) and will eventually produce a matrix of pairwise D2S values (one for each pair of samples) sent to stdout.
google-reverse-image-search 0.5.0
A package to scrape Google Images for image relating to a picture or query
Requires Python: >=3.9

# Google Reverse Image Search

## Installation
Download the `src` folder or download from `pip` with the terminal command (below)

Run the command in your local terminal with a Virtual Environment (https://docs.python.org/3/library/venv.html#creating-virtual-environments)
```sh
> python -m venv your_venv_name

# Downloading from GitHub 
> pip install -r ./path/to/requirements.txt

# Downloading from pip
> pip install google-reverse-image-search

> playwright install chromium
```
Note : Only works for Chrome _(for now but likely won't change)_

## Usage

Import all functions from the file with 
```py
from google_reverse_image_search import google_reverse_search
```

Then start anywhere with the three basic functions

```py
print(google_reverse_search.search_with_query(query="your query"))
print(google_reverse_search.search_with_url(url="https://link/to/photo"),num=5)
print(google_reverse_search.search_with_file(file_path="C:/path/to/file",num=20))
```

## Examples
All three functions will return the images in a similar manner

### Code
```py
res:dict = google_reverse_search.search_with_query(query="boats",num=3)
print(res)
```

### Results
>Formatted for easier reading
```ps1
Connected...
Navigating...
Getting results...
Formatting results...
{'title': 'boats', 
    'data': [
        {'link': 'https://www.discoverboating.com/sites/default/files/small-boats_1.jpg', 'name': 'The Ultimate Guide to Small Boats | Discover Boating', 'dimensions': [1200, 795]}, 
        {'link': 'https://d1nkxkz7ge96ao.cloudfront.net/eyJidWNrZXQiOiJzbW4tbWFpbi1zaXRlLWJ1Y2tldCIsImtleSI6ImltYWdlc1wvaW1hZ2luXC9McktPcmhFcE5FN0FNV3lFQUxRMUpFOE0wTjVsc1VkekxsNU9ZcEZsLmpwZyIsImVkaXRzIjp7InJlc2l6ZSI6eyJ3aWR0aCI6MjYwMCwiaGVpZ2h0IjoxMzAwLCJmaXQiOiJjb3ZlciJ9fX0=', 'name': "Family-Friendly Offshore Center Consoles & Bay Boats from 20' to 35' |  Sportsman Boats", 'dimensions': [2600, 1300]}, 
        {'link': 'https://cdn.britannica.com/27/166127-050-5E3F9372/salmon-fishing-boat-Alaska.jpg', 'name': 'Boat | Definition, History, Types, & Facts | Britannica', 'dimensions': [1600, 1075]}
    ]
}
```

## Bugs and Issues
 Please raise any issues you have on the [Issues](https://github.com/horse-3903/google-reverse-image-search/issues) forum, and I'll take a look and fix it 🙏
shell-piper 0.7.2
Write a temporary file and pass it to a program
Requires Python: >=3.9

# shell-piper

Shell-piper is a commandline program made to write to a temporary file with your
editor and pass that file's contents to an external program through various methods.

## Installation

The recommended way to install shell-piper is through [pipx](https://github.com/pypa/pipx)
(`pipx install shell-piper`). Arch users can also install shell-piper from [the AUR](https://aur.archlinux.org/packages/shell-piper).

You can also clone this repository and build shell-piper manually:

```bash
git clone 'https://github.com/Mrfiregem/shell-piper.git'
cd shell-piper
flit install
```

## Quickstart

### Stdin Mode

Copy and paste text into your editor and modify it with `awk`:

```bash
shellpiper -- awk -F $'\t' '{ print $2 }'
```

### Argument Mode

Convert pasted html into markdown with `pandoc`:

```bash
shellpiper --type argument -- pandoc '{piper:file}' --from html -o converted.md
```

The argument `{piper:file}` will be expanded by shell-piper to the full path of
the temporary file. If this argument is not present, the file path will be appended
as the last argument.

### Expand Mode

Pass a list of urls to download with `youtube-dl`, with each line as an argument:

```bash
shellpiper -t x youtube-dl
```

## Usage

```text
usage: shellpiper [-h] [-v] [-V] [-t TYPE] [-k] program [args ...]

Write a temporary file and pass it to a program

positional arguments:
  program               The program to pass your file to
  args                  Arguments to pass to the program

options:
  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit
  -V, --verbose         Show debug messages
  -t TYPE, --type TYPE  How the file will be given to the program
  -k, --keep-empty      Don't remove empty lines when using '--type expand'

Use '--' to prevent command flags to the right of it being parsed by piper.

The '--type' flag can take values 'stdin' (default), 'argument', or 'expand',
or the letters 's', 'a', or 'x', respectively. This determines how the file is
passed to your program by shellpiper.
```