alleleTools.format.allele2vcf module
Allele Table to VCF Conversion Module.
This module provides functionality to convert allele table data into VCF (Variant Call Format) files. It handles the transformation of genotype data from tabular format to standard VCF format, including proper diploid notation and genomic coordinate mapping.
Author: Nicolás Mendoza Mejía (2023)
- alleleTools.format.allele2vcf.call_function(args)[source]
Main function to execute allele table to VCF conversion.
This function orchestrates the conversion process by: 1. Validating input parameters 2. Loading and processing allele table data 3. Converting to VCF format with proper diploid notation 4. Mapping alleles to genomic coordinates 5. Appending results to the target VCF file
- Parameters:
args – Parsed command line arguments containing: - input: Path to input allele table file - loci_file: Path to gene loci information file - gene_cluster: Alternative gene cluster specification - vcf: Path to target VCF file for appending - field_separator: Field separator for input file (default: tab)
- Raises:
SystemExit – If neither gene_cluster nor loci_file is provided