Metadata-Version: 2.1
Name: gene4mVCF
Version: 1.1.4
Summary: Description of your package
Home-page: https://github.com/VJ-Ulaganathan/gene4mVCF
Author: Pr (France). Dr. rer. nat. Vijay K. ULAGANATHAN
Author-email: vijay-kumar.ulaganathan@uni-tuebingen.de
Description-Content-Type: text/markdown
Requires-Dist: pysam>=0.16.0.1
Requires-Dist: pandas>=1.0.0
Requires-Dist: pybedtools>=0.8.0
Requires-Dist: tqdm>=4.47.0
Requires-Dist: gffutils>=0.10.1

# 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>
  
## 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/VJ-Ulaganathan/gene4mVCF


## Installation

Installation via pip:

`$ pip install gene4mVCF`



