| Name | vcf2fasta JSON |
| Version |
0.1.2
JSON |
| download |
| home_page | None |
| Summary | A package to convert VCF files to FASTA format. |
| upload_time | 2025-07-29 02:35:16 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.10 |
| license | MIT License Copyright (c) 2023 Santiago Sanchez 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: 1. The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. 2. 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. |
| keywords |
vcf
fasta
bioinformatics
genomics
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# vcf2fasta
> **this package is not actively maintained**
## Overview
`vcf2fasta` is a Python package designed to convert genomic regions and intervals into FASTA alignments using VCF files, GFF/GTF files, and a reference FASTA genome. This tool is particularly useful for bioinformaticians and researchers working with genomic data.
## Features
- Convert VCF files to FASTA format.
- Support for GFF/GTF and BED files for feature annotation.
- Options to include reference sequences and handle incomplete CDS.
- Command-line interface for easy usage.
## Installation
To install `vcf2fasta`, you can use pip:
```bash
pip install vcf2fasta
```
## Build
Build the package locally with:
```
python3 -m pip install -e .
```
## Usage
To use `vcf2fasta`, you can run the command line interface with the required arguments. Here is an example:
```bash
vcf2fasta -f genome.fas -v variants.vcf.gz -g intervals.gff -e CDS
```
### Command Line Options
- `-f`, `--fasta`: Path to the reference FASTA file (required).
- `-v`, `--vcf`: Path to the tabix-indexed VCF file (required).
- `-g`, `--gff`: Path to the GFF/GTF file (optional).
- `-b`, `--blend`: Concatenate GFF entries of the specified feature into a single alignment (default: False).
- `-i`, `--inframe`: Force the first codon of the sequence to be inframe (default: False).
- `-o`, `--out`: Name for the output directory (default: "vcf2fasta").
- `-r`, `--addref`: Include the reference sequence in the FASTA alignment (default: False).
- `-s`, `--skip`: Skip features without variants (default: False).
## Contribution
Contributions are welcome! If you would like to contribute to `vcf2fasta`, please fork the repository and submit a pull request. You can also open issues for any bugs or feature requests.
## License
This project is licensed under the MIT License. See the LICENSE file for more details.
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