geno2phenotb

• geno2phenotb package
  • Submodules
  • geno2phenotb.annotate_vcf module
    • annotate_vcf()
  • geno2phenotb.geno2phenotb module
    • main()
    • run()
    • setup_logging()
  • geno2phenotb.installation_test module
    • check_sha256()
    • download_file()
    • download_test_files()
    • self_test()
  • geno2phenotb.parse_args module
    • parse_args()
  • geno2phenotb.predict module
    • adjusted_classes()
    • predict()
    • single_prediction()
  • geno2phenotb.preprocess module
    • collect_lineages()
    • determine_genotype()
    • preprocess()
    • run_mtbseq()
  • geno2phenotb.utils module
    • check_fastq_filenames()
    • check_output()
    • get_amino_ann()
    • get_aminos()
    • get_drugs()
    • get_key_genes()
    • get_lineages()
    • get_rules()
    • get_static_dir()
    • stripper()
  • geno2phenotb.vcf_columns_extractor module
    • vcf_columns_extractor()
  • geno2phenotb.vcf_columns_extractor_geno module
    • vcf_columns_extractor_geno()
  • Module contents