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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:

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:

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.