semvec/pypi-packages huggingface dataset:
fastapi-tarpit 1.0.4
FastAPI middleware that purposely delays incoming connections on unused routes
Requires Python: >=3.10

# FastAPI Tarpit

[FastAPI](https://fastapi.tiangolo.com/) middleware that purposely delays
incoming connections on unused routes.

Definition of a tarpit from [Wikipedia](https://en.wikipedia.org/wiki/Tarpit_(networking)):

> A tarpit is a service on a computer system (usually a server) that purposely delays incoming connections. The technique was developed as a defense against a computer worm, and the idea is that network abuses such as spamming or broad scanning are less effective, and therefore less attractive, if they take too long. The concept is analogous with a tar pit, in which animals can get bogged down and slowly sink under the surface, like in a swamp.

## Installation

Install the package using pip:

```bash
pip install fastapi-tarpit
```

## Usage

```python
from fastapi import FastAPI
from fastapi_tarpit import HTTPTarpitMiddleware

app = FastAPI()

app.add_middleware(HTTPTarpitMiddleware)

@app.get("/foo")
async def foobar():
    return {"foo": "bar"}
```

The code above triggers the tarpit on any other routes than `/foo`, and
routes related to docs.
gene4mVCF 1.1.5
Description of your package

# gene4mVCF

## Introduction
`gene4mVCF` is a Python package that allows you to extract variant entries for specific genes or a list of genes from a VCF (Variant Call Format) file. It utilizes tools like `bcftools`, `tabix`, and Python libraries like `pysam`, `pandas`, `pybedtools`, `tqdm`, and `gffutils` to efficiently parse and extract variants.

## Installation

You can install `gene4mVCF` via pip:

`$ pip install gene4mVCF`

After installation please download the four required bed files and place inside the folder /gene4mVCF
<br>'hg19.ensGene.bed' --> https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/genes/hg19.ensGene.gtf.gz </br>
<br>'hg19.ncbiRefSeq.bed' --> https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/genes/hg19.ncbiRefSeq.gtf.gz </br>
<br>'hg38.ensGene.bed' --> https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/genes/hg38.ensGene.gtf.gz </br>
<br>'hg38.ncbiRefSeq.bed'--> https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/genes/hg38.ncbiRefSeq.gtf.gz </br>

## Usage
Extract variant entries for a specific gene or list of genes from a VCF file.
<br>usage: `$ gene4mVCF [-h] -i INPUT -g GENE [-r REFERENCE]`</br>

Needed arguments:
 <br>`-i INPUT, --input INPUT, is bgzip compressed VCF file`</br>
 <br>`-g GENE, --genes GENE, is either a Gene name, Ensembl gene ID, or path to a genelist file with *.txt extension`</br>


<br>optional arguments:</br>
   <br>`-h, --help show this help message and exit`</br>
   <br>`-r REFERENCE, --ref REFERENCE, is 37 or 38, based on the reference genome used for creating the VCF file`</br>
   <br>`-f FEATURE, --feature FEATURE, is feature type(s) to filter for (e.g., exon, CDS, 5UTR, 3UTR, transcript)`</br>
  
## Examples
Extract variants for a single gene using gene name:
`$ gene4mVCF -i input.vcf.gz -g EGFR`

Extract variants for a single using ensembl gene id:
`$ gene4mVCF -i input.vcf.gz -g ENSG00000168878`

Extract variants for multiple genes listed in a file:
`$ gene4mVCF -i input.vcf.gz -g acmg-genes.txt`

For more options and details, refer to the help message.

**Example showing extraction of variants of ACTB gene**

<br>input command</br>
![Example Image](images/input.png)

<br>Output file in the tab-separated format</br>
![Example Image](images/ACTB.png)


## Support
For any issues or inquiries, please open an issue on the GitHub repository https://github.com/vkulaganathan/gene4mVCF


## Installation

Installation via pip:

`$ pip install gene4mVCF`





<i>current version='1.1.5'</i>