gwas-norm API

• gwas_norm package
  • gwas_norm.gwas_norm
  • gwas_norm.processors
  • gwas_norm.config
    • ASSEMBLY_PREFIX
    • ASSEMBLY_SYN_SECTION
    • CHAIN_FILE_PREFIX
    • CONFIG_DEFAULT_NAME
    • CONFIG_ENV
    • DETAIL_DELIMITER
    • GwasNormConfig
      • GwasNormConfig.as_dict()
      • GwasNormConfig.get_chain_file()
      • GwasNormConfig.get_defaults()
      • GwasNormConfig.get_mapping_file()
      • GwasNormConfig.get_norm_assembly_name()
      • GwasNormConfig.get_ref_assembly()
      • GwasNormConfig.name
    • MAPPING_FILE_SECTION
    • get_config_file()
  • gwas_norm.common
    • ChrPosSpec
      • ChrPosSpec.end_anchor
      • ChrPosSpec.spec_columns
      • ChrPosSpec.start_anchor
    • Msg
      • Msg.msg_args()
      • Msg.msg_prog()
      • Msg.set_file()
      • Msg.set_verbose()
    • add_column_name()
    • bsd_chksum_file()
    • bsd_chksum_str()
    • check_abs_path()
    • check_analysis_type()
    • check_effect_type()
    • check_parent()
    • compress_file()
    • convert()
    • count_lines()
    • create_chrpos_spec_str()
    • create_uni_id()
    • error_on_empty()
    • expand_relative_path()
    • get_column_name()
    • get_file_name()
    • get_old_analysis_id()
    • get_open_method()
    • get_tmp_file()
    • md5_file()
    • norm_name()
    • parse_bool()
    • parse_chrpos_spec_str()
    • passthrough()
    • safe_move()
    • stdopen()
  • gwas_norm.constants
    • ChrPosSpec
      • ChrPosSpec.end_anchor
      • ChrPosSpec.spec_columns
      • ChrPosSpec.start_anchor
    • Msg
      • Msg.msg_args()
      • Msg.msg_prog()
      • Msg.set_file()
      • Msg.set_verbose()
    • add_column_name()
    • bsd_chksum_file()
    • bsd_chksum_str()
    • check_abs_path()
    • check_analysis_type()
    • check_effect_type()
    • check_parent()
    • compress_file()
    • convert()
    • count_lines()
    • create_chrpos_spec_str()
    • create_uni_id()
    • error_on_empty()
    • expand_relative_path()
    • get_column_name()
    • get_file_name()
    • get_old_analysis_id()
    • get_open_method()
    • get_tmp_file()
    • md5_file()
    • norm_name()
    • parse_bool()
    • parse_chrpos_spec_str()
    • passthrough()
    • safe_move()
    • stdopen()
• gwas_norm.metadata sub-package
  • gwas_norm.metadata.gwas_data
    • GwasData
      • GwasData.ROOT_TAG
      • GwasData.n_studies
      • GwasData.get_study_by_name()
      • GwasData.get_analysis_by_name()
      • GwasData.n_analyses
      • GwasData.root_source_dir
      • GwasData.root_norm_dir
      • GwasData.file_check
      • GwasData.studies
      • GwasData.add_study()
      • GwasData.remove_study()
      • GwasData.read()
      • GwasData.write()
      • GwasData.to_xml()
      • GwasData.from_xml()
      • GwasData.get_class()
  • gwas_norm.metadata.study
    • Study
      • Study.CONSORTIUM_TAG
      • Study.METAFILE_TAG
      • Study.PRIVATE_ATTRIBUTE
      • Study.PUBMED_ID_TAG
      • Study.SOURCE_GENOME_ASSEMLY_TAG
      • Study.STUDY_ID_TAG
      • Study.STUDY_NAME_TAG
      • Study.STUDY_NORM_DIR_TAG
      • Study.STUDY_SOURCE_DIR_TAG
      • Study.URL_TAG
      • Study.add_metafile()
      • Study.analyses
      • Study.bind()
      • Study.check_old_analysis_ids()
      • Study.chksum
      • Study.create_analysis_xml()
      • Study.get_analysis_by_name()
      • Study.get_class()
      • Study.info
      • Study.invalidate()
      • Study.invalidate_analyses()
      • Study.is_validated
      • Study.metafile_abspath
      • Study.metafiles
      • Study.name
      • Study.parent
      • Study.private
      • Study.pubmed_id
      • Study.refresh_analysis_data()
      • Study.remove_analysis()
      • Study.repr_attr_str()
      • Study.source_genome_assembly
      • Study.study_id
      • Study.study_name
      • Study.study_norm_absolute_dir
      • Study.study_norm_dir
      • Study.study_source_absolute_dir
      • Study.study_source_dir
      • Study.unbind()
      • Study.ROOT_TAG
      • Study.n_file_holders()
      • Study.file_check
      • Study.validate()
      • Study.add_analysis()
      • Study.to_xml()
      • Study.from_xml()
    • StudyFile
      • StudyFile.ANALYSIS_TYPE_TAG
      • StudyFile.CONSORTIUM_TAG
      • StudyFile.EFFECT_TYPE_TAG
      • StudyFile.FILE_CLASS
      • StudyFile.METAFILE_TAG
      • StudyFile.PRIVATE_ATTRIBUTE
      • StudyFile.PUBMED_ID_TAG
      • StudyFile.SOURCE_GENOME_ASSEMLY_TAG
      • StudyFile.STUDY_ID_TAG
      • StudyFile.STUDY_NAME_TAG
      • StudyFile.STUDY_NORM_DIR_TAG
      • StudyFile.STUDY_SOURCE_DIR_TAG
      • StudyFile.UNITS_TAG
      • StudyFile.URL_TAG
      • StudyFile.add_file()
      • StudyFile.add_metafile()
      • StudyFile.analyses
      • StudyFile.analysis_type
      • StudyFile.bind()
      • StudyFile.check_old_analysis_ids()
      • StudyFile.chksum
      • StudyFile.cohort
      • StudyFile.create_analysis_type_xml()
      • StudyFile.create_analysis_xml()
      • StudyFile.create_cohort_xml()
      • StudyFile.create_effect_type_xml()
      • StudyFile.create_files_xml()
      • StudyFile.create_units_xml()
      • StudyFile.create_xml()
      • StudyFile.effect_type
      • StudyFile.file_check
      • StudyFile.file_repr_attr_str()
      • StudyFile.files
      • StudyFile.get_analysis_by_name()
      • StudyFile.get_class()
      • StudyFile.info
      • StudyFile.init_file_attr()
      • StudyFile.invalidate()
      • StudyFile.invalidate_analyses()
      • StudyFile.is_validated
      • StudyFile.metafile_abspath
      • StudyFile.metafiles
      • StudyFile.n_files
      • StudyFile.name
      • StudyFile.parent
      • StudyFile.parse_files()
      • StudyFile.parse_xml()
      • StudyFile.private
      • StudyFile.pubmed_id
      • StudyFile.refresh_analysis_data()
      • StudyFile.remove_files()
      • StudyFile.repr_attr_str()
      • StudyFile.source_genome_assembly
      • StudyFile.study_id
      • StudyFile.study_name
      • StudyFile.study_norm_absolute_dir
      • StudyFile.study_norm_dir
      • StudyFile.study_source_absolute_dir
      • StudyFile.study_source_dir
      • StudyFile.unbind()
      • StudyFile.units
      • StudyFile.ROOT_TAG
      • StudyFile.validate()
      • StudyFile.n_file_holders()
      • StudyFile.on_file_added()
      • StudyFile.on_files_removed()
      • StudyFile.add_analysis()
      • StudyFile.remove_analysis()
      • StudyFile.to_xml()
      • StudyFile.from_xml()
  • gwas_norm.metadata.analysis
    • KeyAnalysis
      • KeyAnalysis.ROOT_TAG
      • KeyAnalysis.KEY_TAG
      • KeyAnalysis.ANALYSIS_ID_TAG
      • KeyAnalysis.ANALYSIS_NAME_TAG
      • KeyAnalysis.add_test()
      • KeyAnalysis.analysis_id
      • KeyAnalysis.analysis_name
      • KeyAnalysis.bind()
      • KeyAnalysis.caveat
      • KeyAnalysis.chksum
      • KeyAnalysis.get_class()
      • KeyAnalysis.has_caveat
      • KeyAnalysis.has_phenotype
      • KeyAnalysis.has_test()
      • KeyAnalysis.info
      • KeyAnalysis.info_columns
      • KeyAnalysis.info_defs
      • KeyAnalysis.invalidate()
      • KeyAnalysis.is_validated
      • KeyAnalysis.n_tests
      • KeyAnalysis.name
      • KeyAnalysis.parent
      • KeyAnalysis.parse_caveats()
      • KeyAnalysis.parse_info_data()
      • KeyAnalysis.parse_phenotypes()
      • KeyAnalysis.parse_tests()
      • KeyAnalysis.phenotype
      • KeyAnalysis.tests
      • KeyAnalysis.unbind()
      • KeyAnalysis.VALUE_TAG
      • KeyAnalysis.repr_attr_str()
      • KeyAnalysis.keys
      • KeyAnalysis.add_key()
      • KeyAnalysis.validate()
      • KeyAnalysis.to_xml()
      • KeyAnalysis.from_xml()
    • AnalysisFile
      • AnalysisFile.ANALYSIS_ID_TAG
      • AnalysisFile.ANALYSIS_NAME_TAG
      • AnalysisFile.ANALYSIS_TYPE_TAG
      • AnalysisFile.EFFECT_TYPE_TAG
      • AnalysisFile.FILE_CLASS
      • AnalysisFile.UNITS_TAG
      • AnalysisFile.add_file()
      • AnalysisFile.add_test()
      • AnalysisFile.analysis_id
      • AnalysisFile.analysis_name
      • AnalysisFile.analysis_type
      • AnalysisFile.bind()
      • AnalysisFile.caveat
      • AnalysisFile.chksum
      • AnalysisFile.cohort
      • AnalysisFile.create_analysis_type_xml()
      • AnalysisFile.create_cohort_xml()
      • AnalysisFile.create_effect_type_xml()
      • AnalysisFile.create_files_xml()
      • AnalysisFile.create_units_xml()
      • AnalysisFile.create_xml()
      • AnalysisFile.effect_type
      • AnalysisFile.file_check
      • AnalysisFile.file_repr_attr_str()
      • AnalysisFile.files
      • AnalysisFile.get_class()
      • AnalysisFile.has_caveat
      • AnalysisFile.has_phenotype
      • AnalysisFile.has_test()
      • AnalysisFile.info
      • AnalysisFile.info_columns
      • AnalysisFile.info_defs
      • AnalysisFile.init_file_attr()
      • AnalysisFile.invalidate()
      • AnalysisFile.is_validated
      • AnalysisFile.n_files
      • AnalysisFile.n_tests
      • AnalysisFile.name
      • AnalysisFile.parent
      • AnalysisFile.parse_caveats()
      • AnalysisFile.parse_files()
      • AnalysisFile.parse_info_data()
      • AnalysisFile.parse_phenotypes()
      • AnalysisFile.parse_tests()
      • AnalysisFile.parse_xml()
      • AnalysisFile.phenotype
      • AnalysisFile.remove_files()
      • AnalysisFile.tests
      • AnalysisFile.unbind()
      • AnalysisFile.units
      • AnalysisFile.ROOT_TAG
      • AnalysisFile.validate()
      • AnalysisFile.study_source_absolute_dir
      • AnalysisFile.repr_attr_str()
      • AnalysisFile.on_file_added()
      • AnalysisFile.to_xml()
      • AnalysisFile.from_xml()
  • gwas_norm.metadata.phenotype
    • Phenotype
      • Phenotype.ROOT_TAG
      • Phenotype.from_xml()
      • Phenotype.REFERENCE_STRING_TAG
      • Phenotype.definition
      • Phenotype.flat_definition
      • Phenotype.get_class()
      • Phenotype.info_defs
      • Phenotype.reference_string
      • Phenotype.to_xml()
    • Caveat
      • Caveat.ROOT_TAG
      • Caveat.from_xml()
      • Caveat.REFERENCE_STRING_TAG
      • Caveat.definition
      • Caveat.flat_definition
      • Caveat.get_class()
      • Caveat.info_defs
      • Caveat.reference_string
      • Caveat.to_xml()
    • Definition
      • Definition.ROOT_TAG
      • Definition.UNDEF_TYPE
      • Definition.reference_string
      • Definition.flat_definition
      • Definition.to_xml()
      • Definition.from_xml()
      • Definition.get_class()
      • Definition.DATA_TYPE_ATTRIBUTE
      • Definition.INFO_ATTRIBUTE
      • Definition.MAP_TO_ATTRIBUTE
      • Definition.dstruct
      • Definition.dtype
      • Definition.equals()
      • Definition.get_attributes()
      • Definition.info
      • Definition.init_info_values()
      • Definition.map_to
      • Definition.set_attributes()
    • Synonym
      • Synonym.ROOT_TAG
      • Synonym.reference_string
      • Synonym.flat_definition
      • Synonym.synonyms
      • Synonym.add()
      • Synonym.to_xml()
      • Synonym.from_xml()
      • Synonym.get_class()
    • And
      • And.contents
      • And.flat_definition
      • And.get_class()
      • And.parse_xml()
      • And.to_xml()
      • And.ROOT_TAG
      • And.reference_string
      • And.add()
      • And.from_xml()
    • Or
      • Or.contents
      • Or.flat_definition
      • Or.get_class()
      • Or.parse_xml()
      • Or.to_xml()
      • Or.ROOT_TAG
      • Or.reference_string
      • Or.add()
      • Or.from_xml()
  • gwas_norm.metadata.cohort
    • SampleSizeMixin
      • SampleSizeMixin.TYPE
      • SampleSizeMixin.N_SAMPLES_TAG
      • SampleSizeMixin.n_samples
      • SampleSizeMixin.create_nsamples_xml()
      • SampleSizeMixin.parse_xml()
      • SampleSizeMixin.PROPORTION_TYPE
      • SampleSizeMixin.REAL_TYPE
      • SampleSizeMixin.reset_seen_values()
      • SampleSizeMixin.value_type
    • CaseControlMixin
      • CaseControlMixin.TYPE
      • CaseControlMixin.N_CASES_TAG
      • CaseControlMixin.N_CONTROLS_TAG
      • CaseControlMixin.n_samples
      • CaseControlMixin.n_cases
      • CaseControlMixin.n_controls
      • CaseControlMixin.create_case_xml()
      • CaseControlMixin.parse_xml()
      • CaseControlMixin.PROPORTION_TYPE
      • CaseControlMixin.REAL_TYPE
      • CaseControlMixin.reset_seen_values()
      • CaseControlMixin.value_type
    • LdReference
      • LdReference.ROOT_TAG
      • LdReference.NAME_TAG
      • LdReference.REF_POP_TAG
      • LdReference.WEIGHT_TAG
      • LdReference.add_pop()
      • LdReference.from_xml()
      • LdReference.get_class()
      • LdReference.name
      • LdReference.pops
      • LdReference.refpops
      • LdReference.remove_pop()
      • LdReference.reset_pops()
      • LdReference.to_xml()
      • LdReference.weight
    • FreqReference
      • FreqReference.ROOT_TAG
      • FreqReference.NAME_TAG
      • FreqReference.REF_POP_TAG
      • FreqReference.WEIGHT_TAG
      • FreqReference.add_pop()
      • FreqReference.from_xml()
      • FreqReference.get_class()
      • FreqReference.name
      • FreqReference.pops
      • FreqReference.refpops
      • FreqReference.remove_pop()
      • FreqReference.reset_pops()
      • FreqReference.to_xml()
      • FreqReference.weight
    • Population
      • Population.ROOT_TAG
      • Population.TYPE
      • Population.NAME_TAG
      • Population.freq_pops
      • Population.ld_pops
      • Population.add_ld_pop()
      • Population.add_freq_pop()
      • Population.remove_ld_pop()
      • Population.remove_freq_pop()
      • Population.reset_ld_pops()
      • Population.reset_freq_pops()
      • Population.to_xml()
      • Population.from_xml()
      • Population.get_class()
    • CaseControlPopulation
      • CaseControlPopulation.ROOT_TAG
      • CaseControlPopulation.n_cases
      • CaseControlPopulation.n_controls
      • CaseControlPopulation.to_xml()
      • CaseControlPopulation.NAME_TAG
      • CaseControlPopulation.N_CASES_TAG
      • CaseControlPopulation.N_CONTROLS_TAG
      • CaseControlPopulation.PROPORTION_TYPE
      • CaseControlPopulation.REAL_TYPE
      • CaseControlPopulation.TYPE
      • CaseControlPopulation.add_freq_pop()
      • CaseControlPopulation.add_ld_pop()
      • CaseControlPopulation.create_case_xml()
      • CaseControlPopulation.freq_pops
      • CaseControlPopulation.from_xml()
      • CaseControlPopulation.get_class()
      • CaseControlPopulation.ld_pops
      • CaseControlPopulation.n_samples
      • CaseControlPopulation.parse_xml()
      • CaseControlPopulation.remove_freq_pop()
      • CaseControlPopulation.remove_ld_pop()
      • CaseControlPopulation.reset_freq_pops()
      • CaseControlPopulation.reset_ld_pops()
      • CaseControlPopulation.reset_seen_values()
      • CaseControlPopulation.value_type
    • SamplePopulation
      • SamplePopulation.ROOT_TAG
      • SamplePopulation.n_samples
      • SamplePopulation.to_xml()
      • SamplePopulation.NAME_TAG
      • SamplePopulation.N_SAMPLES_TAG
      • SamplePopulation.PROPORTION_TYPE
      • SamplePopulation.REAL_TYPE
      • SamplePopulation.TYPE
      • SamplePopulation.add_freq_pop()
      • SamplePopulation.add_ld_pop()
      • SamplePopulation.create_nsamples_xml()
      • SamplePopulation.freq_pops
      • SamplePopulation.from_xml()
      • SamplePopulation.get_class()
      • SamplePopulation.ld_pops
      • SamplePopulation.parse_xml()
      • SamplePopulation.remove_freq_pop()
      • SamplePopulation.remove_ld_pop()
      • SamplePopulation.reset_freq_pops()
      • SamplePopulation.reset_ld_pops()
      • SamplePopulation.reset_seen_values()
      • SamplePopulation.value_type
    • Cohort
      • Cohort.ROOT_TAG
      • Cohort.NAME_TAG
      • Cohort.TYPE
      • Cohort.n_samples
      • Cohort.pops
      • Cohort.name
      • Cohort.add_population()
      • Cohort.to_xml()
      • Cohort.from_xml()
      • Cohort.get_class()
    • CaseControlCohort
      • CaseControlCohort.NAME_TAG
      • CaseControlCohort.N_CASES_TAG
      • CaseControlCohort.N_CONTROLS_TAG
      • CaseControlCohort.PROPORTION_TYPE
      • CaseControlCohort.REAL_TYPE
      • CaseControlCohort.TYPE
      • CaseControlCohort.create_case_xml()
      • CaseControlCohort.from_xml()
      • CaseControlCohort.get_class()
      • CaseControlCohort.n_samples
      • CaseControlCohort.name
      • CaseControlCohort.parse_xml()
      • CaseControlCohort.pops
      • CaseControlCohort.reset_seen_values()
      • CaseControlCohort.value_type
      • CaseControlCohort.ROOT_TAG
      • CaseControlCohort.n_cases
      • CaseControlCohort.n_controls
      • CaseControlCohort.add_population()
      • CaseControlCohort.to_xml()
    • SampleCohort
      • SampleCohort.NAME_TAG
      • SampleCohort.N_SAMPLES_TAG
      • SampleCohort.PROPORTION_TYPE
      • SampleCohort.REAL_TYPE
      • SampleCohort.TYPE
      • SampleCohort.create_nsamples_xml()
      • SampleCohort.from_xml()
      • SampleCohort.get_class()
      • SampleCohort.name
      • SampleCohort.parse_xml()
      • SampleCohort.pops
      • SampleCohort.reset_seen_values()
      • SampleCohort.value_type
      • SampleCohort.ROOT_TAG
      • SampleCohort.n_samples
      • SampleCohort.add_population()
      • SampleCohort.to_xml()
  • gwas_norm.metadata.file
    • FileHolderMixin
      • FileHolderMixin.EFFECT_TYPE_TAG
      • FileHolderMixin.ANALYSIS_TYPE_TAG
      • FileHolderMixin.UNITS_TAG
      • FileHolderMixin.FILE_CLASS
      • FileHolderMixin.file_repr_attr_str()
      • FileHolderMixin.init_file_attr()
      • FileHolderMixin.cohort
      • FileHolderMixin.files
      • FileHolderMixin.n_files
      • FileHolderMixin.file_check
      • FileHolderMixin.analysis_type
      • FileHolderMixin.effect_type
      • FileHolderMixin.units
      • FileHolderMixin.add_file()
      • FileHolderMixin.remove_files()
      • FileHolderMixin.create_effect_type_xml()
      • FileHolderMixin.create_analysis_type_xml()
      • FileHolderMixin.create_units_xml()
      • FileHolderMixin.create_files_xml()
      • FileHolderMixin.create_cohort_xml()
      • FileHolderMixin.create_xml()
      • FileHolderMixin.parse_xml()
      • FileHolderMixin.parse_files()
    • GwasFile
      • GwasFile.ROOT_TAG
      • GwasFile.RELATIVE_PATH_TAG
      • GwasFile.MD5_TAG
      • GwasFile.COMMENT_CHAR_TAG
      • GwasFile.SKIPLINES_TAG
      • GwasFile.PVALUE_LOGGED_TAG
      • GwasFile.COMPRESSION_TAG
      • GwasFile.ENCODING_TAG
      • GwasFile.CHR_POS_SPEC_TAG
      • GwasFile.COLUMNS_TAG
      • GwasFile.HAS_HEADER_TAG
      • GwasFile.KEYS_TAG
      • GwasFile.INFO_ATTRIBUTE
      • GwasFile.MAP_TO_ATTRIBUTE
      • GwasFile.CSV_DOUBLE_QUOTE_TAG
      • GwasFile.CSV_ESCAPE_CHAR_TAG
      • GwasFile.CSV_QUOTE_CHAR_TAG
      • GwasFile.CSV_QUOTING_TAG
      • GwasFile.CSV_SKIP_INIT_WHITESPACE_TAG
      • GwasFile.CSV_STRICT_TAG
      • GwasFile.CSV_LINE_TERMINATOR_TAG
      • GwasFile.CSV_DELIMITER_TAG
      • GwasFile.is_validated
      • GwasFile.validate()
      • GwasFile.invalidate()
      • GwasFile.csv_kwargs
      • GwasFile.has_header
      • GwasFile.header_is_known
      • GwasFile.header
      • GwasFile.normaliser
      • GwasFile.compression
      • GwasFile.skiplines
      • GwasFile.chrpos_spec
      • GwasFile.column_map
      • GwasFile.md5_chksum
      • GwasFile.is_checked
      • GwasFile.absolute_path
      • GwasFile.basename
      • GwasFile.relative_path
      • GwasFile.keys
      • GwasFile.info
      • GwasFile.info_columns
      • GwasFile.set_header()
      • GwasFile.check_file()
      • GwasFile.bind()
      • GwasFile.unbind()
      • GwasFile.to_xml()
      • GwasFile.from_xml()
      • GwasFile.get_class()
  • gwas_norm.metadata.test
    • Test
      • Test.ROOT_TAG
      • Test.CHR_NAME_TAG
      • Test.START_POS_TAG
      • Test.EFFECT_TYPE_TAG
      • Test.EFFECT_SIZE_TAG
      • Test.EFFECT_ALLELE_TAG
      • Test.VAR_ID_TAG
      • Test.OTHER_ALLELE_TAG
      • Test.STANDARD_ERROR_TAG
      • Test.PVALUE_TAG
      • Test.PVALUE_LOGGED_TAG
      • Test.EFFECT_SIZE_DELTA
      • Test.STANDARD_ERROR_DELTA
      • Test.LOG10_PVALUE_DELTA
      • Test.TEST_PASS
      • Test.TEST_FAIL
      • Test.TestResult
      • Test.test_row()
      • Test.test_chr_name()
      • Test.test_start_pos()
      • Test.test_effects()
      • Test.test_standard_error()
      • Test.test_pvalue()
      • Test.test_var_id()
      • Test.to_xml()
      • Test.from_xml()
      • Test.get_class()
  • gwas_norm.metadata.info
    • Info
      • Info.ROOT_TAG
      • Info.columns
      • Info.definitions
      • Info.add_column()
      • Info.remove_column()
      • Info.add_definition()
      • Info.remove_definition()
      • Info.to_xml()
      • Info.from_xml()
      • Info.get_class()
  • gwas_norm.metadata.column
    • Column
      • Column.ROOT_TAG
      • Column.name
      • Column.to_xml()
      • Column.from_xml()
      • Column.get_class()
      • Column.DATA_TYPE_ATTRIBUTE
      • Column.INFO_ATTRIBUTE
      • Column.MAP_TO_ATTRIBUTE
      • Column.dstruct
      • Column.dtype
      • Column.equals()
      • Column.get_attributes()
      • Column.info
      • Column.init_info_values()
      • Column.map_to
      • Column.set_attributes()
    • MappingColumn
      • MappingColumn.ROOT_TAG
      • MappingColumn.to_xml()
      • MappingColumn.DATA_TYPE_ATTRIBUTE
      • MappingColumn.INFO_ATTRIBUTE
      • MappingColumn.MAP_TO_ATTRIBUTE
      • MappingColumn.dstruct
      • MappingColumn.dtype
      • MappingColumn.equals()
      • MappingColumn.from_xml()
      • MappingColumn.get_attributes()
      • MappingColumn.info
      • MappingColumn.init_info_values()
      • MappingColumn.map_to
      • MappingColumn.name
      • MappingColumn.set_attributes()
      • MappingColumn.get_class()
  • gwas_norm.metadata.convert
    • convert_xml()
• gwas_norm.utils sub-package
  • gwas_norm.utils.genome_chunks
    • convert_bgi_to_text()
    • create_chunk_file()
    • find_in_header()
    • get_chunks()
    • get_end_pos()
    • get_ref_end_pos()
  • gwas_norm.utils.quick_lift
• gwas_norm.variants sub-package
  • gwas_norm.variants.vcf_info
    • ALLELE
    • CADD_INFO_FIELD
    • CADD_KEY_LOOKUP
    • CADD_MAIN_DELIMITER
    • CADD_PHRED
    • CADD_RAW
    • CLINORIGIN_BI
    • CLINORIGIN_DEN
    • CLINORIGIN_GERM
    • CLINORIGIN_INC
    • CLINORIGIN_INH
    • CLINORIGIN_LOOKUP
    • CLINORIGIN_MAT
    • CLINORIGIN_NT
    • CLINORIGIN_OTH
    • CLINORIGIN_PAT
    • CLINORIGIN_SOM
    • CLINORIGIN_UNI
    • CLINORIGIN_UNKN
    • CLINSIG_AFF
    • CLINSIG_ASSC
    • CLINSIG_BEN
    • CLINSIG_CONF
    • CLINSIG_DRUG
    • CLINSIG_ERR
    • CLINSIG_LBEN
    • CLINSIG_LOOKUP
    • CLINSIG_LPATH
    • CLINSIG_NP
    • CLINSIG_OTH
    • CLINSIG_PATH
    • CLINSIG_PROT
    • CLINSIG_RISK
    • CLINSIG_SEN
    • CLINSIG_USIG
    • CLINVAR_ID_DELIMITER
    • CLINVAR_MAIN_DELIMITER
    • CLINVAR_MAPPED_FIELDS
    • CLINVAR_ORIGIN
    • CLINVAR_SIGNIF
    • CLINVAR_SUB_DELIMITER
    • CLNACC
    • CLNDISDB
    • CLNDN
    • CLNHGVS
    • CLNORIGIN
    • CLNREVSTAT
    • CLNSIG
    • CLNVI
    • CODING_SEQUENCE
    • CONSEQUENCE
    • CONSEQUENCES
    • CONSEQUENCE_LOOKUP
    • CaddKeys
      • CaddKeys.cadd_name
      • CaddKeys.key_name
      • CaddKeys.parser
    • ClinVarKeys
      • ClinVarKeys.clinvar_name
      • ClinVarKeys.key_name
      • ClinVarKeys.parser
    • ClinVarOri
      • ClinVarOri.display_name
      • ClinVarOri.int
      • ClinVarOri.name
    • ClinVarSig
      • ClinVarSig.display_name
      • ClinVarSig.int
      • ClinVarSig.name
      • ClinVarSig.rank
    • DOWNSTREAM
    • FEATURE
    • FEATURE_ELONGATION
    • FEATURE_TYPE
    • FEAT_TRUNCATION
    • FIVE_PRIME_UTR
    • FRAMESHIFT
    • GENE
    • INCOMPLETE_TERMINAL_CODON
    • INFRAME_DEL
    • INFRAME_INS
    • INTERGENIC
    • INTRON
    • MATURE_MIRNA
    • MISSENSE
    • NC_TRANS
    • NC_TRANS_EXON
    • NMD_TRANS
    • POLYPHEN
    • PROT_ALTERING
    • REG_REGION
    • REG_REGION_ABLATION
    • REG_REGION_AMP
    • SIFT
    • SPLICE_ACCEPTOR
    • SPLICE_DONOR
    • SPLICE_DONOR_FIFTH_BASE
    • SPLICE_DONOR_REGION
    • SPLICE_POLYPRIM_TRACT
    • SPLICE_REGION
    • START_LOST
    • START_RETAINED
    • STOP_GAINED
    • STOP_LOST
    • STOP_RETAINED
    • SYNONYMOUS
    • So
      • So.description
      • So.display_name
      • So.id
      • So.impact
      • So.name
      • So.rank
    • TFBS_ABLATION
    • TFBS_AMP
    • TF_BINDING_SITE
    • THREE_PRIME_UTR
    • TRANS_ABLATION
    • TRANS_AMP
    • UPSTREAM
    • VCF_MISSING
    • VEP_INFO_FIELD
    • VEP_KEY_LOOKUP
    • VEP_MAIN_DELIMITER
    • VepKeys
      • VepKeys.key_name
      • VepKeys.parser
      • VepKeys.vep_name
    • cadd_info_parser()
    • clinvar_most_significant()
    • parse_clinvar()
    • parse_clinvar_dbs()
    • parse_clinvar_delim()
    • parse_clinvar_disease_db()
    • parse_clinvar_origin()
    • parse_clinvar_significance()
    • parse_clinvar_var_id()
    • parse_float()
    • parse_none()
    • parse_return()
    • parse_vep_consequence()
    • validate_header_metadata()
    • vep_info_parser()
    • vep_worst_consequence()
  • gwas_norm.variants.norm
    • EnsemblRefNorm
      • EnsemblRefNorm.close()
      • EnsemblRefNorm.open()
      • EnsemblRefNorm.search_assembly()
    • RefNorm
      • RefNorm.cache_ref_assembly_match()
      • RefNorm.close()
      • RefNorm.get_minimal_alleles()
      • RefNorm.normalise_alleles()
      • RefNorm.normalise_multi_alleles()
      • RefNorm.open()
      • RefNorm.ref_assembly_match()
      • RefNorm.search_assembly()
      • RefNorm.valid_ref()
    • test_coords()
  • gwas_norm.variants.mapper
    • BaseMapper
      • BaseMapper.DNA_REGEXP
      • BaseMapper.best_mapping()
      • BaseMapper.close()
      • BaseMapper.decode_mapping_flags()
      • BaseMapper.get_mapping_error()
      • BaseMapper.get_mapping_var_id()
      • BaseMapper.get_no_data_mapping()
      • BaseMapper.map_variant()
      • BaseMapper.open()
      • BaseMapper.order_mappings()
      • BaseMapper.quick_match()
      • BaseMapper.resolver
      • BaseMapper.sort_map()
      • BaseMapper.validate_resolver()
      • BaseMapper.var_id_match()
    • EnsemblVariantMapper
      • EnsemblVariantMapper.DNA_REGEXP
      • EnsemblVariantMapper.get_mapping_var_id()
      • EnsemblVariantMapper.map_variant()
      • EnsemblVariantMapper.query_region()
    • ScanVcfVariantMapper
      • ScanVcfVariantMapper.DNA_REGEX
      • ScanVcfVariantMapper.MAPPING_FILE_TYPE
      • ScanVcfVariantMapper.check_new_chr_name()
      • ScanVcfVariantMapper.check_norm()
      • ScanVcfVariantMapper.close()
      • ScanVcfVariantMapper.extract_alt_allele()
      • ScanVcfVariantMapper.extract_nothing()
      • ScanVcfVariantMapper.extract_positive_strand()
      • ScanVcfVariantMapper.extract_strand()
      • ScanVcfVariantMapper.extract_var_id()
      • ScanVcfVariantMapper.get_buffer_sort_key()
      • ScanVcfVariantMapper.get_mapping_join_key()
      • ScanVcfVariantMapper.get_mapping_var_id()
      • ScanVcfVariantMapper.get_source_join_key()
      • ScanVcfVariantMapper.header
      • ScanVcfVariantMapper.init_mapping_file()
      • ScanVcfVariantMapper.init_source_file()
      • ScanVcfVariantMapper.map_variant()
      • ScanVcfVariantMapper.mapping_correct()
      • ScanVcfVariantMapper.open()
      • ScanVcfVariantMapper.output_sorted
      • ScanVcfVariantMapper.sort_buffer()
      • ScanVcfVariantMapper.source
      • ScanVcfVariantMapper.test_sort_order()
      • ScanVcfVariantMapper.validate_resolver()
    • TabixVcfVariantMapper
      • TabixVcfVariantMapper.close()
      • TabixVcfVariantMapper.get_mapping_var_id()
      • TabixVcfVariantMapper.map_variant()
      • TabixVcfVariantMapper.open()
    • VcfIterator
      • VcfIterator.close()
      • VcfIterator.open()
    • allele_idx()
    • get_mapping_coords()
    • map_data_frame()
    • return_none()
    • reverse_complement()
    • split_alts()
    • variant_type()
    • vcf_to_ensembl()
  • gwas_norm.variants.resolvers
    • BaseResolver
      • BaseResolver.DEFAULT_INTERNAL_DELIMITER
      • BaseResolver.METADATA_SUMMARY_ROW_HEADER
      • BaseResolver.MIN_ALT_IMPUTE_EVIDENCE
      • BaseResolver.extract_metadata()
      • BaseResolver.extract_summary_metadata_row()
      • BaseResolver.get_mapping_error()
      • BaseResolver.get_no_data_mapping()
      • BaseResolver.impute_alt_allele()
      • BaseResolver.resolve_poor_mapping()
      • BaseResolver.sort_map()
      • BaseResolver.validate_data_source()
    • EnsemblResolver
      • EnsemblResolver.METADATA_SUMMARY_ROW_HEADER
      • EnsemblResolver.cache
      • EnsemblResolver.extract_metadata()
      • EnsemblResolver.extract_summary_metadata_row()
      • EnsemblResolver.get_alt_allele_freq()
      • EnsemblResolver.impute_alt_allele()
      • EnsemblResolver.list_populations()
      • EnsemblResolver.query_allele_freq()
      • EnsemblResolver.resolve_poor_mapping()
      • EnsemblResolver.validate_data_source()
      • EnsemblResolver.validate_populations()
    • MappingFileResolver
      • MappingFileResolver.METADATA_SUMMARY_ROW_HEADER
      • MappingFileResolver.extract_cadd()
      • MappingFileResolver.extract_datasets()
      • MappingFileResolver.extract_id()
      • MappingFileResolver.extract_metadata()
      • MappingFileResolver.extract_pops()
      • MappingFileResolver.extract_summary_metadata_row()
      • MappingFileResolver.extract_vep()
      • MappingFileResolver.impute_alt_allele()
      • MappingFileResolver.list_populations()
      • MappingFileResolver.validate_cadd_format()
      • MappingFileResolver.validate_data_source()
      • MappingFileResolver.validate_header_format()
      • MappingFileResolver.validate_population_kwarg()
      • MappingFileResolver.validate_populations()
      • MappingFileResolver.validate_vep_format()
    • PopulationResolver
      • PopulationResolver.ALLOWED_ALLELE_FREQ
      • PopulationResolver.HIER_AAF
      • PopulationResolver.MEAN_AAF
      • PopulationResolver.METADATA_SUMMARY_ROW_HEADER
      • PopulationResolver.extract_hierarchy_aaf_counts()
      • PopulationResolver.extract_hierarchy_aaf_freq()
      • PopulationResolver.extract_mean_aaf_counts()
      • PopulationResolver.extract_mean_aaf_freq()
      • PopulationResolver.extract_no_aaf()
      • PopulationResolver.list_populations()
      • PopulationResolver.validate_population_kwarg()
  • gwas_norm.variants.constants
    • ALLELE_DELIMITER
    • DNA
    • ALLOWED_TYPES
    • BLANK_ALLELE
    • ID
    • CHR
    • START
    • END
    • STRAND
    • REF
    • ALT
    • STRAND_FLIP
    • REF_FLIP
    • PARTIAL_ALLELE_MATCH
    • COORD_OFFSET
    • MAPPING_DECODE
    • MAPPING_DECODE_STR
    • ALT
    • ALT_ALLELE_INFERRED
    • BALANCED
    • CHR
    • COMP_TRANSLATE
    • Column
      • Column.alias
      • Column.expected_idx
      • Column.name
    • DELETION
    • DNA_DEL_REGEX
    • DNA_DEL_STR
    • DNA_REGEX
    • DNA_STR
    • DataSet
      • DataSet.bits
      • DataSet.name
    • END
    • ENSEMBL_DELETION
    • ENS_ID_REGEX
    • ENS_ID_STR
    • ERROR
    • FLAGS
    • ID
    • INSERTION
    • IS_PALINDROMIC
    • MapCoord
      • MapCoord.alt_allele
      • MapCoord.chr_name
      • MapCoord.ref_allele
      • MapCoord.start_pos
      • MapCoord.strand
    • MappingFlag
      • MappingFlag.bits
      • MappingFlag.description
      • MappingFlag.name
    • MappingResult
      • MappingResult.errors
      • MappingResult.map_bits
      • MappingResult.map_row
      • MappingResult.mapping_coords
      • MappingResult.nsites
      • MappingResult.resolver
      • MappingResult.source_coords
      • MappingResult.source_row
    • NORMALISED
    • NO_DATA
    • PARTIAL_ALLELE_MATCH
    • POP_START_IDX
    • REF
    • REF_FLIP
    • RS_REGEX
    • RS_STR
    • START
    • STRAND
    • STRAND_FLIP
    • UNKNOWN_INDEL
    • VCF_FORMAT_IDX
    • VCF_ID_IDX
    • VCF_INFO_IDX
    • dataset_bits()
    • decode_mapping_flags()
    • main()
  • gwas_norm.variants.common
    • SequenceError
    • get_end_pos()
    • get_uni_id()
    • skip_vcf_header()
    • split_alt()
• gwas_norm.variants.downloads sub-package
  • gwas_norm.variants.downloads.format_dbsnp
    • parse_dbsnp_vcf()
  • gwas_norm.variants.downloads.format_alfa
    • parse_alfa_vcf()
  • gwas_norm.variants.downloads.format_snpstats
    • parse_snpstats()
  • gwas_norm.variants.downloads.fix_split_counts
    • fix_vcf_split_counts()
  • gwas_norm.variants.downloads.merge_cadd
    • merge_cadd_files()
  • gwas_norm.variants.downloads.merge_counts
    • merge_count_files()
  • gwas_norm.variants.downloads.split_mapping
    • split_mapping_file()
• gwas_norm.hpc sub-package
  • gwas_norm.hpc.hpc_gwas_norm