Index

A

add() (alleleTools.allele.FieldTree method) add_batch() (alleleTools.allele.FieldTree method) add_out_altable_args() (in module alleleTools.argtypes) adjustFigAspect() (in module alleleTools.plot.graph_pathogens) Allele (class in alleleTools.allele) AlleleMatchStatus (class in alleleTools.allele) AlleleParsedTable (class in alleleTools.format.allele_resolution) AlleleParser (class in alleleTools.allele) alleles (alleleTools.format.alleleTable.AlleleTable attribute) AlleleTable (class in alleleTools.format.alleleTable) alleleTools module alleleTools.allele module alleleTools.alleleTools module alleleTools.argtypes module alleleTools.format module alleleTools.format.allele2vcf module alleleTools.format.allele_resolution module alleleTools.format.alleleTable module alleleTools.format.from_ikmb_hla module alleleTools.format.gene_report module alleleTools.format.hla_group module alleleTools.format.immuannot_report module alleleTools.format.kir_mapper module alleleTools.format.tests module

alleleTools.format.tests.test_consensus module alleleTools.format.tests.test_gene_report module alleleTools.format.tests.test_hla_group module alleleTools.format.tests.test_ukb2allele module alleleTools.format.tests.test_vcf2allele module alleleTools.format.ukb2allele module alleleTools.format.vcf module alleleTools.format.vcf2allele module alleleTools.plot module alleleTools.plot.graph_pathogens module alleleTools.plot.graph_phewas module alleleTools.plot.plot_ikmb_coverage module alleleTools.tests module alleleTools.tests.test_allele module alleleTools.tests.test_argtypes module alleleTools.utils module alleleTools.utils.assets module asdict() (alleleTools.format.gene_report.Gene method) aslist() (alleleTools.format.gene_report.Report method)

B

build_allele_tree() (in module alleleTools.tests.test_allele)

C

call_function() (in module alleleTools.format.allele2vcf) (in module alleleTools.format.allele_resolution) (in module alleleTools.format.from_ikmb_hla) (in module alleleTools.format.hla_group) (in module alleleTools.format.immuannot_report) (in module alleleTools.format.kir_mapper) (in module alleleTools.format.ukb2allele) (in module alleleTools.format.vcf2allele) (in module alleleTools.plot.graph_pathogens) (in module alleleTools.plot.graph_phewas) (in module alleleTools.plot.plot_ikmb_coverage) check_dir_writable() (in module alleleTools.argtypes)

children (alleleTools.allele.FieldTree attribute) compare() (alleleTools.allele.Allele method) confidence (alleleTools.allele.Allele attribute) consensus() (alleleTools.format.from_ikmb_hla.ConsensusReport method) consensus_dict() (alleleTools.format.from_ikmb_hla.ConsensusGene method) ConsensusGene (class in alleleTools.format.from_ikmb_hla) ConsensusReport (class in alleleTools.format.from_ikmb_hla) convert_to_altable() (alleleTools.format.allele_resolution.AlleleParsedTable method) covariates (alleleTools.format.alleleTable.AlleleTable attribute) coverage() (alleleTools.format.tests.test_gene_report.TestGeneConsensus method) create_phewas_plot() (in module alleleTools.plot.graph_phewas) csv_file() (in module alleleTools.argtypes)

D

dataframe (alleleTools.format.vcf.VCF attribute) DelimitedParser (class in alleleTools.allele)

df (alleleTools.format.vcf2allele.VCFalleles attribute) download_file() (in module alleleTools.utils.assets)

E

EQUAL (alleleTools.allele.AlleleMatchStatus attribute)

exclude_high_missings() (in module alleleTools.format.kir_mapper)

F

field (alleleTools.allele.FieldTree attribute) fields (alleleTools.allele.Allele attribute)

FieldTree (class in alleleTools.allele) file_path() (in module alleleTools.argtypes)

G

gene (alleleTools.allele.Allele attribute) Gene (class in alleleTools.format.gene_report) get_asset_path() (in module alleleTools.utils.assets) get_attributes() (alleleTools.format.immuannot_report.GTF method) get_consensus() (alleleTools.allele.FieldTree method) get_consensus_call() (alleleTools.format.from_ikmb_hla.ConsensusGene method) get_delimiters() (alleleTools.allele.AlleleParser method)

get_fields() (alleleTools.allele.Allele method) get_file_list() (in module alleleTools.format.immuannot_report) get_format() (alleleTools.format.vcf.VCF method) get_min_number() (in module alleleTools.format.kir_mapper) get_results_as_df() (in module alleleTools.format.immuannot_report) graph_by_genus() (in module alleleTools.plot.graph_pathogens) GrouperHLA (class in alleleTools.format.hla_group) GTF (class in alleleTools.format.immuannot_report)

L

LESS_RESOLUTION (alleleTools.allele.AlleleMatchStatus attribute) load_phenotype() (alleleTools.format.alleleTable.AlleleTable method)

lookup() (alleleTools.format.hla_group.GrouperHLA method) lookup_exact() (alleleTools.format.hla_group.GrouperHLA method) lookup_partial() (alleleTools.format.hla_group.GrouperHLA method)

M

main() (in module alleleTools.alleleTools) make_report() (in module alleleTools.format.tests.test_consensus) mean_coverage() (alleleTools.format.gene_report.Gene method) merge_tree() (alleleTools.allele.FieldTree method) metadata (alleleTools.format.vcf.VCF attribute) module alleleTools alleleTools.allele alleleTools.alleleTools alleleTools.argtypes alleleTools.format alleleTools.format.allele2vcf alleleTools.format.allele_resolution alleleTools.format.alleleTable alleleTools.format.from_ikmb_hla alleleTools.format.gene_report alleleTools.format.hla_group alleleTools.format.immuannot_report alleleTools.format.kir_mapper alleleTools.format.tests alleleTools.format.tests.test_consensus alleleTools.format.tests.test_gene_report alleleTools.format.tests.test_hla_group alleleTools.format.tests.test_ukb2allele alleleTools.format.tests.test_vcf2allele alleleTools.format.ukb2allele alleleTools.format.vcf alleleTools.format.vcf2allele alleleTools.plot alleleTools.plot.graph_pathogens alleleTools.plot.graph_phewas alleleTools.plot.plot_ikmb_coverage alleleTools.tests alleleTools.tests.test_allele alleleTools.tests.test_argtypes alleleTools.utils alleleTools.utils.assets

MORE_RESOLUTION (alleleTools.allele.AlleleMatchStatus attribute)

N

normalize_resolution() (alleleTools.format.allele_resolution.AlleleParsedTable method)

NOT_EQUAL (alleleTools.allele.AlleleMatchStatus attribute)

O

open() (alleleTools.format.allele_resolution.AlleleParsedTable class method) (alleleTools.format.alleleTable.AlleleTable class method)

output_path() (in module alleleTools.argtypes)

P

parse() (alleleTools.allele.AlleleParser method) (alleleTools.allele.DelimitedParser method) (alleleTools.allele.ParsingStrategy method) (alleleTools.allele.RegexParser method) parse_alleles() (alleleTools.format.allele_resolution.AlleleParsedTable method) (alleleTools.tests.test_allele.TestFieldTree method) (in module alleleTools.format.kir_mapper)

parse_attribute() (alleleTools.format.immuannot_report.GTF method) parser (alleleTools.tests.test_allele.TestHlaAllele attribute) ParsingStrategy (class in alleleTools.allele) path() (in module alleleTools.argtypes) phenotype (alleleTools.format.alleleTable.AlleleTable attribute) print_progress_bar() (in module alleleTools.format.immuannot_report) process_gtf_file() (in module alleleTools.format.immuannot_report)

Q

queue_files() (in module alleleTools.format.immuannot_report)

quick_lookup() (in module alleleTools.format.hla_group)

R

read_input_files() (in module alleleTools.format.immuannot_report) read_json() (in module alleleTools.format.gene_report) read_reports() (in module alleleTools.format.kir_mapper) read_reports_asdf() (in module alleleTools.plot.plot_ikmb_coverage) RegexParser (class in alleleTools.allele)

remove_HLA_prefix() (in module alleleTools.format.gene_report) remove_id_prefix() (alleleTools.format.vcf.VCF method) remove_phenotype_zero() (alleleTools.format.alleleTable.AlleleTable method) Report (class in alleleTools.format.gene_report) reports_as_allele_table() (in module alleleTools.format.from_ikmb_hla)

S

samples() (alleleTools.format.vcf.VCF method) samples_dataframe() (alleleTools.format.vcf.VCF method) save() (alleleTools.format.vcf.VCF method) set_consensus_settings() (alleleTools.format.from_ikmb_hla.ConsensusGene method) set_gene_family() (alleleTools.allele.AlleleParser method) set_phenotype() (alleleTools.format.alleleTable.AlleleTable method) set_support() (alleleTools.allele.FieldTree method) setup_parser() (in module alleleTools.format) (in module alleleTools.format.allele2vcf) (in module alleleTools.format.allele_resolution) (in module alleleTools.format.from_ikmb_hla) (in module alleleTools.format.hla_group) (in module alleleTools.format.immuannot_report) (in module alleleTools.format.kir_mapper) (in module alleleTools.format.ukb2allele) (in module alleleTools.format.vcf2allele) (in module alleleTools.plot) (in module alleleTools.plot.graph_pathogens) (in module alleleTools.plot.graph_phewas) (in module alleleTools.plot.plot_ikmb_coverage)

Solution (class in alleleTools.allele) sort_and_fill() (alleleTools.format.vcf2allele.VCFalleles method) split_alleles() (in module alleleTools.format.kir_mapper) support (alleleTools.allele.FieldTree attribute)

T

test_1allele_1field() (alleleTools.tests.test_allele.TestFieldTree method) test_1allele_2fields() (alleleTools.tests.test_allele.TestFieldTree method) test_1allele_3fields() (alleleTools.tests.test_allele.TestFieldTree method) test_1allele_4fields() (alleleTools.tests.test_allele.TestFieldTree method) test_2f_allele_grouping() (in module alleleTools.format.tests.test_hla_group) test_3f_allele_grouping() (in module alleleTools.format.tests.test_hla_group) test_allele_counting_fist_level() (alleleTools.tests.test_allele.TestFieldTree method) test_allele_counting_second_level() (alleleTools.tests.test_allele.TestFieldTree method) test_allele_counting_second_level_minor_allele() (alleleTools.tests.test_allele.TestFieldTree method) test_allele_formatting() (in module alleleTools.format.tests.test_ukb2allele) test_allele_parsing() (alleleTools.tests.test_allele.TestHlaAllele method) (alleleTools.tests.test_allele.TestKirAllele method) test_allele_sorting() (in module alleleTools.format.tests.test_consensus) test_allele_support_homozygous() (alleleTools.tests.test_allele.TestFieldTree method) test_comparison_results() (alleleTools.tests.test_allele.TestHlaAllele method) test_consensus() (in module alleleTools.format.tests.test_consensus) test_convert_ukb_to_allele() (in module alleleTools.format.tests.test_ukb2allele) test_default_parser() (alleleTools.tests.test_allele.TestAlleleParser method) test_delimited_parsing() (alleleTools.tests.test_allele.TestAlleleParser method) test_fail() (alleleTools.tests.test_argtypes.TestOutputPath method) test_file_already_exists() (alleleTools.tests.test_argtypes.TestOutputPath method) test_fill_allele_pairs() (in module alleleTools.format.tests.test_ukb2allele) test_fill_allele_pairs_unsorted() (in module alleleTools.format.tests.test_ukb2allele) test_gene_asdict() (in module alleleTools.format.tests.test_gene_report)

test_gene_mean_coverage() (in module alleleTools.format.tests.test_gene_report) test_hla_hisat_parsing() (alleleTools.tests.test_allele.TestAlleleParser method) test_hla_parsing() (alleleTools.tests.test_allele.TestAlleleParser method) test_no_gene_name() (alleleTools.format.tests.test_gene_report.TestGeneConsensus method) test_ok() (alleleTools.tests.test_argtypes.TestOutputPath method) test_one_allele() (alleleTools.tests.test_allele.TestFieldTree method) test_only_dir_without_file() (alleleTools.tests.test_argtypes.TestOutputPath method) test_only_file_in_current_dir() (alleleTools.tests.test_argtypes.TestOutputPath method) test_overlapping_allele_consensus() (in module alleleTools.format.tests.test_consensus) test_read_reports_asdf() (in module alleleTools.format.tests.test_gene_report) test_read_vcf() (in module alleleTools.format.tests.test_vcf2allele) test_remove_HLA_prefix() (in module alleleTools.format.tests.test_gene_report) test_remove_pheno_zero() (in module alleleTools.format.tests.test_ukb2allele) test_report_aslist() (in module alleleTools.format.tests.test_gene_report) test_similar_calls() (alleleTools.format.tests.test_gene_report.TestGeneConsensus method) test_wrong_parser() (alleleTools.tests.test_allele.TestAlleleParser method) TestAlleleParser (class in alleleTools.tests.test_allele) TestFieldTree (class in alleleTools.tests.test_allele) TestGeneConsensus (class in alleleTools.format.tests.test_gene_report) TestHlaAllele (class in alleleTools.tests.test_allele) TestKirAllele (class in alleleTools.tests.test_allele) TestOutputPath (class in alleleTools.tests.test_argtypes) to_csv() (alleleTools.format.allele_resolution.AlleleParsedTable method) (alleleTools.format.alleleTable.AlleleTable method) truncate() (alleleTools.allele.Allele method)

V

VCF (class in alleleTools.format.vcf)

VCFalleles (class in alleleTools.format.vcf2allele)

W

worker() (in module alleleTools.format.immuannot_report)