biophony 1.2.1

Random generation of genetic files

Genetic data files generator for testing purposes

biophony is a package for generating random genetic data files intended specifically for testing and validation. Real genetic data is often too large, lacks flexibility, or raises privacy concerns, making it unsuitable for thorough testing. biophony makes it simpler to test software in different scenarios without needing real data, enabling focused and efficient development and validation.

Installation

biophony requires at least Python 3.11 to work.

To install with pip, run:

pip install biophony

Usage

Command Line Interfaces

biophony provides the following CLIs to generate data:

• gen-cov: generates a BED file with custom depth,
• gen-fasta: generates a FASTA file with a custom size sequence,
• gen-fastavar: generates a FASTA file with custom size sequences, each with n variants with control over insertion, deletion and mutation rate,
• gen-fastq: generates a FASTQ file with custom read count and size,
• gen-vcf: generates a VCF file from a FASTA file, with control over insertion, deletion and mutation rate.

CLIs that read and / or write data do it on stdin and stdout by default, thus permitting to chain operations with the pipe operator |.

For exemple, run the following command to generate a VCF with 2% SNP, 1% INS and 1% DEL:

gen-fasta | gen-vcf --snp-rate 0.02 --ins-rate 0.01 --del-rate 0.01

To save the generated content, you can either use the regular output operator > to redirect stdout to a file or use the dedicated option:

gen-fasta | gen-vcf --snp-rate 0.02 --ins-rate 0.01 --del-rate 0.01 > test.vcf  # redirect
gen-fasta | gen-vcf --snp-rate 0.02 --ins-rate 0.01 --del-rate 0.01 -o test.vcf  # dedicated option

Python API

You can also use the Python API to generate random genetic data files in your scripts.

Link to the Python API documentation: https://cnrgh.gitlab.io/databases/biophony/.

NEWS

1.2.1 - 2024-11-18

• Fix Invalid cross-device link error that occurred with gen-vcf, in environments where /tmp and the VCF output parent directory (--output-vcf option) were not on the same partition / filesystem. This error was occurring in the GitLab CI pipeline.

1.2.0 - 2024-11-18

• Provide type annotations by adding a py.typed marker file.
• Export MutSim class to allow generation of VCF files in scripts.
• Generate documentation with sphinx and sphinx-autoapi.
• Improve README.md.

1.1.0 - 2024-08-10

• Allow to output gzipped files with gen-fasta and gen-fastq.
• New gen-fastq script to generate FASTQ files.

1.0.1 - 2024-05-30

• gen-vcf: correct usage of file path to pass to mutation-simulator.
• gen-fasta: disable header tag line (comment line) by default.