Index

A

adjusted_classes() (in module geno2phenotb.predict)

annotate_vcf() (in module geno2phenotb.annotate_vcf)

C

check_fastq_filenames() (in module geno2phenotb.utils) check_output() (in module geno2phenotb.utils)

check_sha256() (in module geno2phenotb.installation_test) collect_lineages() (in module geno2phenotb.preprocess)

D

determine_genotype() (in module geno2phenotb.preprocess)

download_file() (in module geno2phenotb.installation_test) download_test_files() (in module geno2phenotb.installation_test)

G

geno2phenotb module geno2phenotb.annotate_vcf module geno2phenotb.geno2phenotb module geno2phenotb.installation_test module geno2phenotb.parse_args module geno2phenotb.predict module geno2phenotb.preprocess module

geno2phenotb.utils module geno2phenotb.vcf_columns_extractor module geno2phenotb.vcf_columns_extractor_geno module get_amino_ann() (in module geno2phenotb.utils) get_aminos() (in module geno2phenotb.utils) get_drugs() (in module geno2phenotb.utils) get_key_genes() (in module geno2phenotb.utils) get_lineages() (in module geno2phenotb.utils) get_rules() (in module geno2phenotb.utils) get_static_dir() (in module geno2phenotb.utils)

M

main() (in module geno2phenotb.geno2phenotb) module geno2phenotb geno2phenotb.annotate_vcf geno2phenotb.geno2phenotb geno2phenotb.installation_test geno2phenotb.parse_args geno2phenotb.predict geno2phenotb.preprocess geno2phenotb.utils geno2phenotb.vcf_columns_extractor geno2phenotb.vcf_columns_extractor_geno

P

parse_args() (in module geno2phenotb.parse_args)

predict() (in module geno2phenotb.predict) preprocess() (in module geno2phenotb.preprocess)

R

run() (in module geno2phenotb.geno2phenotb)

run_mtbseq() (in module geno2phenotb.preprocess)

S

self_test() (in module geno2phenotb.installation_test) setup_logging() (in module geno2phenotb.geno2phenotb)

single_prediction() (in module geno2phenotb.predict) stripper() (in module geno2phenotb.utils)

V

vcf_columns_extractor() (in module geno2phenotb.vcf_columns_extractor)

vcf_columns_extractor_geno() (in module geno2phenotb.vcf_columns_extractor_geno)