sbsgenerator

SBSGenerator

SBSGenerator is a comprehensive Python package designed for bioinformaticians and researchers working in the field of genomics. This package offers a robust set of tools for generating, analyzing, and interpreting single base substitutions (SBS) mutations from Variant Call Format (VCF) files. With a focus on ease of use, efficiency, and scalability, SBSGenerator facilitates the detailed study of genomic mutations, aiding in the understanding of their roles in various biological processes and diseases. Uniquely developed using a hybrid of Python and Rust, SBSGenerator leverages the PyO3 library for seamless integration between Python's flexible programming capabilities and Rust's unparalleled performance. This innovative approach ensures that SBSGenerator is not only user-friendly but also incredibly efficient and capable of handling large-scale genomic data with ease.

Installation

$ pip install sbsgenerator

Usage

The SBSGenerator package is designed to facilitate the generation and analysis of SBS mutation data from VCF files across different genomic contexts. Depending on the specified context size, it can create comprehensive dataframes listing all possible SBS mutations, ranging from simple 3-nucleotide contexts to more complex 7-nucleotide contexts, with the potential number of mutation combinations exponentially increasing with context size.

• Context 3: The dataframe contains all of the following the pyrimidine single nucleotide variants, N[{C > A, G, or T} or {T > A, G, or C}]N. 4 possible starting nucleotides x 6 pyrimidine variants x 4 ending nucleotides = 96 total combinations.

• Context 5: The dataframe contains all of the following the pyrimidine single nucleotide variants, NN[{C > A, G, or T} or {T > A, G, or C}]NN. 16 (4x4) possible starting nucleotides x 6 pyrimidine variants x 16 (4x4) possible ending nucleotides = 1536 total combinations.

• Context 7: The dataframe contains all of the following the pyrimidine single nucleotide variants, NNN[{C > A, G, or T} or {T > A, G, or C}]NNN. 64 (4x4x4) nucleotides x 6 pyrimidine variants x 64 (4x4x4) possible ending dinucleotides = 24576 total combinations.

VCF INPUT FILE FORMAT

This tool currently only supports vcf formats. The user must provide variant data adhering to the format. The input VCF (Variant Call Format) file should adhere to the following format:

Name	Fullname	Datatypes
Type	Represents the type of mutation.	str
Gene	Indicates the specific gene associated with the mutation.	str
PMID	Refers to the PubMed ID of the associated research paper.	str
Genome	Specifies the genome version used for mapping.	str
Mutation Type	Describes the type of mutation.	str
Chromosome	Represents the chromosome number where the mutation occurs.	str
Start Position	Indicates the starting position of the mutation on the chromosome.	str
End Position	Represents the ending position of the mutation on the chromosome.	str
Reference Allele	Denotes the original allele at the mutation site.	str
Mutant Allele	Represents the altered allele resulting from the mutation.	str
Method	Describes the method used for mutation detection.	str

from sbsgenerator import generator
# Context number (must be larger than 3 and uneven)
context_size = 7
# List with all the vcf files
vcf_files = ["data/test.vcf"]
# Where the ref genomes will be downloaded to
ref_genome = "temp/ref_genomes"
sbsgen = generator.SBSGenerator(
    context=context_size,
    vcf_files=vcf_files,
    ref_genome=ref_genome
)
sbsgen.count_mutations()
# The attribute count_samples holds the sbs matrix
sbsgen.count_samples

Contributing

I welcome contributions to SBSGenerator! If you have suggestions for improvements or bug fixes, please open an issue or submit a pull request.

License

SBSGenerator is released under the MIT License. See the LICENSE file for more details.