sbsgenerator 1.0.5

Description:

sbsgenerator 1.0.5

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.