alleleTools.format package

Convert module for alleleTools.

This module converts allele data between different file formats including VCF, CSV, and custom allele table formats. It supports conversions from various sources including UK Biobank data and standard genomic formats.

alleleTools.format.setup_parser(subparsers)

Set up the argument parser for the convert subcommand.

Creates a subparser for the ‘convert’ command and registers all available conversion types as sub-subcommands.

Parameters:

subparsers – The subparsers object from the main argument parser.

Returns:

The configured parser for the convert command.

Return type:

argparse.ArgumentParser

Subpackages

• alleleTools.format.tests package
  • Submodules

Submodules

• alleleTools.format.allele2vcf module
  • call_function()
  • setup_parser()
• alleleTools.format.alleleTable module
  • AlleleTable
• alleleTools.format.allele_resolution module
  • AlleleParsedTable
  • call_function()
  • setup_parser()
• alleleTools.format.from_ikmb_hla module
  • ConsensusGene
  • ConsensusReport
  • call_function()
  • reports_as_allele_table()
  • setup_parser()
• alleleTools.format.gene_report module
  • Gene
  • Report
  • read_json()
  • remove_HLA_prefix()
• alleleTools.format.hla_group module
  • GrouperHLA
  • call_function()
  • quick_lookup()
  • setup_parser()
• alleleTools.format.immuannot_report module
  • GTF
  • call_function()
  • get_file_list()
  • get_results_as_df()
  • print_progress_bar()
  • process_gtf_file()
  • queue_files()
  • read_input_files()
  • setup_parser()
  • worker()
• alleleTools.format.kir_mapper module
  • call_function()
  • exclude_high_missings()
  • get_min_number()
  • parse_alleles()
  • read_reports()
  • setup_parser()
  • split_alleles()
• alleleTools.format.ukb2allele module
  • call_function()
  • setup_parser()
• alleleTools.format.vcf module
  • VCF
• alleleTools.format.vcf2allele module
  • VCFalleles
  • call_function()
  • setup_parser()