Index

_

__get_pydantic_core_schema__() (elsheeto.models.utils.CaseInsensitiveDict class method) __init__() (elsheeto.models.aviti.AvitiSheetBuilder method) (elsheeto.models.illumina_v1.IlluminaSheetBuilder method) (elsheeto.models.utils.CaseInsensitiveDict method) (elsheeto.parser.aviti.Parser method) (elsheeto.parser.illumina_v1.Parser method) (elsheeto.parser.stage1.Parser method) (elsheeto.parser.stage2.Parser method)

A

add_read_length() (elsheeto.models.illumina_v1.IlluminaSheetBuilder method) add_run_value() (elsheeto.models.aviti.AvitiSheetBuilder method) add_run_values() (elsheeto.models.aviti.AvitiSheetBuilder method) add_sample() (elsheeto.models.aviti.AvitiSheetBuilder method) (elsheeto.models.illumina_v1.IlluminaSheetBuilder method) add_samples() (elsheeto.models.aviti.AvitiSheetBuilder method) (elsheeto.models.illumina_v1.IlluminaSheetBuilder method) add_setting() (elsheeto.models.aviti.AvitiSheetBuilder method) (elsheeto.models.illumina_v1.IlluminaSheetBuilder method) add_settings() (elsheeto.models.aviti.AvitiSheetBuilder method) (elsheeto.models.illumina_v1.IlluminaSheetBuilder method)

application (elsheeto.models.illumina_v1.IlluminaHeader attribute) assay (elsheeto.models.illumina_v1.IlluminaHeader attribute) AUTO (elsheeto.parser.common.CsvDelimiter attribute) AvitiRunValues (class in elsheeto.models.aviti) AvitiSample (class in elsheeto.models.aviti) AvitiSettingEntries (class in elsheeto.models.aviti) AvitiSettingEntry (class in elsheeto.models.aviti) AvitiSettings (class in elsheeto.models.aviti) AvitiSheet (class in elsheeto.models.aviti) AvitiSheetBuilder (class in elsheeto.models.aviti)

B

build() (elsheeto.models.aviti.AvitiSheetBuilder method) (elsheeto.models.illumina_v1.IlluminaSheetBuilder method)

C

candidate_delimiters() (elsheeto.parser.common.CsvDelimiter method) CaseInsensitiveDict (class in elsheeto.models.utils) chemistry (elsheeto.models.illumina_v1.IlluminaHeader attribute) clear_header_fields() (elsheeto.models.illumina_v1.IlluminaSheetBuilder method) clear_read_lengths() (elsheeto.models.illumina_v1.IlluminaSheetBuilder method) clear_run_values() (elsheeto.models.aviti.AvitiSheetBuilder method) clear_samples() (elsheeto.models.aviti.AvitiSheetBuilder method) (elsheeto.models.illumina_v1.IlluminaSheetBuilder method)

clear_settings() (elsheeto.models.aviti.AvitiSheetBuilder method) (elsheeto.models.illumina_v1.IlluminaSheetBuilder method) column_consistency (elsheeto.parser.common.ParserConfiguration attribute) ColumnConsistency (class in elsheeto.parser.common) ColumnConsistencyWarning COMMA (elsheeto.parser.common.CsvDelimiter attribute) comment_prefixes (elsheeto.parser.common.ParserConfiguration attribute) copy() (elsheeto.models.utils.CaseInsensitiveDict method) CsvDelimiter (class in elsheeto.parser.common)

D

data (elsheeto.models.aviti.AvitiRunValues attribute) (elsheeto.models.aviti.AvitiSettings property) (elsheeto.models.csv_stage1.ParsedRawSection attribute) (elsheeto.models.csv_stage2.DataSection attribute) (elsheeto.models.illumina_v1.IlluminaSampleSheet attribute) (elsheeto.models.illumina_v1.IlluminaSettings attribute) data_section (elsheeto.models.csv_stage2.ParsedSheet attribute)

DataSection (class in elsheeto.models.csv_stage2) date (elsheeto.models.illumina_v1.IlluminaHeader attribute) delimiter (elsheeto.models.csv_stage1.ParsedRawSheet attribute) (elsheeto.models.csv_stage2.ParsedSheet attribute) (elsheeto.parser.common.ParserConfiguration attribute) description (elsheeto.models.aviti.AvitiSample attribute) (elsheeto.models.illumina_v1.IlluminaHeader attribute) (elsheeto.models.illumina_v1.IlluminaSample attribute)

E

elsheeto.exceptions module elsheeto.facade module elsheeto.models.aviti module elsheeto.models.common module elsheeto.models.csv_stage1 module elsheeto.models.csv_stage2 module elsheeto.models.illumina_v1 module elsheeto.models.utils module elsheeto.parser.aviti module

elsheeto.parser.common module elsheeto.parser.illumina_v1 module elsheeto.parser.stage1 module elsheeto.parser.stage2 module ElsheetoException ElsheetoWarning entries (elsheeto.models.aviti.AvitiSettingEntries attribute) experiment_name (elsheeto.models.illumina_v1.IlluminaHeader attribute) external_id (elsheeto.models.aviti.AvitiSample attribute) extra_metadata (elsheeto.models.aviti.AvitiRunValues attribute) (elsheeto.models.aviti.AvitiSample attribute) (elsheeto.models.aviti.AvitiSettings attribute) (elsheeto.models.illumina_v1.IlluminaHeader attribute) (elsheeto.models.illumina_v1.IlluminaSample attribute) (elsheeto.models.illumina_v1.IlluminaSettings attribute)

F

from_csv() (in module elsheeto.parser.stage1) from_sheet() (elsheeto.models.aviti.AvitiSheetBuilder class method) (elsheeto.models.illumina_v1.IlluminaSheetBuilder class method)

from_stage1() (in module elsheeto.parser.stage2) from_stage2() (in module elsheeto.parser.aviti) (in module elsheeto.parser.illumina_v1) fromkeys() (elsheeto.models.utils.CaseInsensitiveDict class method)

G

get_all_by_key() (elsheeto.models.aviti.AvitiSettingEntries method) get_all_lanes() (elsheeto.models.aviti.AvitiSettings method) get_by_key() (elsheeto.models.aviti.AvitiSettingEntries method)

get_by_key_and_lane() (elsheeto.models.aviti.AvitiSettingEntries method) get_settings_by_lane() (elsheeto.models.aviti.AvitiSettings method) getkey() (elsheeto.models.utils.CaseInsensitiveDict method)

H

header (elsheeto.models.illumina_v1.IlluminaSampleSheet attribute) header_sections (elsheeto.models.csv_stage2.ParsedSheet attribute)

header_to_index (elsheeto.models.csv_stage2.DataSection attribute) headers (elsheeto.models.csv_stage2.DataSection attribute) HeaderSection (class in elsheeto.models.csv_stage2)

I

i5_index_id (elsheeto.models.illumina_v1.IlluminaSample attribute) i7_index_id (elsheeto.models.illumina_v1.IlluminaSample attribute) iem_file_version (elsheeto.models.illumina_v1.IlluminaHeader attribute) ignore_empty_lines (elsheeto.parser.common.ParserConfiguration attribute) IlluminaHeader (class in elsheeto.models.illumina_v1) IlluminaReads (class in elsheeto.models.illumina_v1) IlluminaSample (class in elsheeto.models.illumina_v1) IlluminaSampleSheet (class in elsheeto.models.illumina_v1) IlluminaSettings (class in elsheeto.models.illumina_v1)

IlluminaSheetBuilder (class in elsheeto.models.illumina_v1) index (elsheeto.models.illumina_v1.IlluminaSample attribute) index1 (elsheeto.models.aviti.AvitiSample attribute) index2 (elsheeto.models.aviti.AvitiSample attribute) (elsheeto.models.illumina_v1.IlluminaSample attribute) index_adapters (elsheeto.models.illumina_v1.IlluminaHeader attribute) index_plate_well (elsheeto.models.illumina_v1.IlluminaSample attribute) inline_id (elsheeto.models.illumina_v1.IlluminaSample attribute) instrument_type (elsheeto.models.illumina_v1.IlluminaHeader attribute) investigator_name (elsheeto.models.illumina_v1.IlluminaHeader attribute)

K

key_values (elsheeto.models.csv_stage2.HeaderSection property)

L

lane (elsheeto.models.aviti.AvitiSample attribute) (elsheeto.models.aviti.AvitiSettingEntry attribute) (elsheeto.models.illumina_v1.IlluminaSample attribute) LeadingSectionedCsvWarning LOGGER (in module elsheeto.parser.aviti) (in module elsheeto.parser.illumina_v1) (in module elsheeto.parser.stage1) (in module elsheeto.parser.stage2)

LOOSE (elsheeto.parser.common.ColumnConsistency attribute) lower_items() (elsheeto.models.utils.CaseInsensitiveDict method)

M

model_config (elsheeto.models.aviti.AvitiRunValues attribute) (elsheeto.models.aviti.AvitiSample attribute) (elsheeto.models.aviti.AvitiSettingEntries attribute) (elsheeto.models.aviti.AvitiSettingEntry attribute) (elsheeto.models.aviti.AvitiSettings attribute) (elsheeto.models.aviti.AvitiSheet attribute) (elsheeto.models.csv_stage1.ParsedRawSection attribute) (elsheeto.models.csv_stage1.ParsedRawSheet attribute) (elsheeto.models.csv_stage2.DataSection attribute) (elsheeto.models.csv_stage2.HeaderSection attribute) (elsheeto.models.csv_stage2.ParsedSheet attribute) (elsheeto.models.illumina_v1.IlluminaHeader attribute) (elsheeto.models.illumina_v1.IlluminaReads attribute) (elsheeto.models.illumina_v1.IlluminaSample attribute) (elsheeto.models.illumina_v1.IlluminaSampleSheet attribute) (elsheeto.models.illumina_v1.IlluminaSettings attribute) (elsheeto.parser.common.ParserConfiguration attribute)

module elsheeto.exceptions elsheeto.facade elsheeto.models.aviti elsheeto.models.common elsheeto.models.csv_stage1 elsheeto.models.csv_stage2 elsheeto.models.illumina_v1 elsheeto.models.utils elsheeto.parser.aviti elsheeto.parser.common elsheeto.parser.illumina_v1 elsheeto.parser.stage1 elsheeto.parser.stage2

N

name (elsheeto.models.aviti.AvitiSettingEntry attribute) (elsheeto.models.csv_stage1.ParsedRawSection attribute) (elsheeto.models.csv_stage2.HeaderSection attribute)

num_columns (elsheeto.models.csv_stage1.ParsedRawSection attribute)

P

PAD (elsheeto.parser.common.ColumnConsistency attribute) parse() (elsheeto.parser.aviti.Parser method) (elsheeto.parser.illumina_v1.Parser method) (elsheeto.parser.stage1.Parser method) (elsheeto.parser.stage2.Parser method) parse_aviti() (in module elsheeto.facade) parse_aviti_from_data() (in module elsheeto.facade) parse_illumina_v1() (in module elsheeto.facade) parse_illumina_v1_from_data() (in module elsheeto.facade)

ParsedRawSection (class in elsheeto.models.csv_stage1) ParsedRawSheet (class in elsheeto.models.csv_stage1) ParsedSheet (class in elsheeto.models.csv_stage2) ParsedSheetType (class in elsheeto.models.common) Parser (class in elsheeto.parser.aviti) (class in elsheeto.parser.illumina_v1) (class in elsheeto.parser.stage1) (class in elsheeto.parser.stage2) ParserConfiguration (class in elsheeto.parser.common) project (elsheeto.models.aviti.AvitiSample attribute)

R

RawCsvException read_lengths (elsheeto.models.illumina_v1.IlluminaReads attribute) reads (elsheeto.models.illumina_v1.IlluminaSampleSheet attribute) remove_run_value() (elsheeto.models.aviti.AvitiSheetBuilder method) remove_sample() (elsheeto.models.aviti.AvitiSheetBuilder method) (elsheeto.models.illumina_v1.IlluminaSheetBuilder method) remove_sample_by_id() (elsheeto.models.illumina_v1.IlluminaSheetBuilder method) remove_sample_by_name() (elsheeto.models.aviti.AvitiSheetBuilder method)

remove_samples_by_project() (elsheeto.models.aviti.AvitiSheetBuilder method) (elsheeto.models.illumina_v1.IlluminaSheetBuilder method) remove_setting() (elsheeto.models.illumina_v1.IlluminaSheetBuilder method) remove_settings_by_name() (elsheeto.models.aviti.AvitiSheetBuilder method) remove_settings_by_name_and_lane() (elsheeto.models.aviti.AvitiSheetBuilder method) require_section_headers (elsheeto.parser.common.ParserConfiguration attribute) rows (elsheeto.models.csv_stage2.HeaderSection attribute) run (elsheeto.models.illumina_v1.IlluminaHeader attribute) run_values (elsheeto.models.aviti.AvitiSheet attribute)

S

sample_id (elsheeto.models.illumina_v1.IlluminaSample attribute) sample_name (elsheeto.models.aviti.AvitiSample attribute) (elsheeto.models.illumina_v1.IlluminaSample attribute) sample_plate (elsheeto.models.illumina_v1.IlluminaSample attribute) sample_project (elsheeto.models.illumina_v1.IlluminaSample attribute) sample_well (elsheeto.models.illumina_v1.IlluminaSample attribute) samples (elsheeto.models.aviti.AvitiSheet attribute) SECTIONED (elsheeto.models.common.ParsedSheetType attribute) SECTIONLESS (elsheeto.models.common.ParsedSheetType attribute) sections (elsheeto.models.csv_stage1.ParsedRawSheet attribute) SEMICOLON (elsheeto.parser.common.CsvDelimiter attribute) set_header() (elsheeto.models.illumina_v1.IlluminaSheetBuilder method)

set_header_field() (elsheeto.models.illumina_v1.IlluminaSheetBuilder method) set_header_fields() (elsheeto.models.illumina_v1.IlluminaSheetBuilder method) set_read_lengths() (elsheeto.models.illumina_v1.IlluminaSheetBuilder method) set_reads() (elsheeto.models.illumina_v1.IlluminaSheetBuilder method) set_settings() (elsheeto.models.illumina_v1.IlluminaSheetBuilder method) settings (elsheeto.models.aviti.AvitiSettings attribute) (elsheeto.models.aviti.AvitiSheet attribute) (elsheeto.models.illumina_v1.IlluminaSampleSheet attribute) sheet_type (elsheeto.models.csv_stage1.ParsedRawSheet attribute) (elsheeto.models.csv_stage2.ParsedSheet attribute) STRICT_GLOBAL (elsheeto.parser.common.ColumnConsistency attribute) STRICT_SECTIONED (elsheeto.parser.common.ColumnConsistency attribute)

T

TAB (elsheeto.parser.common.CsvDelimiter attribute)

to_csv() (elsheeto.models.aviti.AvitiSheet method) (elsheeto.models.illumina_v1.IlluminaSampleSheet method)

U

update_header_field() (elsheeto.models.illumina_v1.IlluminaSheetBuilder method) update_reads() (elsheeto.models.illumina_v1.IlluminaSheetBuilder method) update_sample() (elsheeto.models.illumina_v1.IlluminaSheetBuilder method)

update_sample_by_id() (elsheeto.models.illumina_v1.IlluminaSheetBuilder method) update_sample_by_name() (elsheeto.models.aviti.AvitiSheetBuilder method) update_settings_field() (elsheeto.models.illumina_v1.IlluminaSheetBuilder method)

V

validate_index1() (elsheeto.models.aviti.AvitiSample class method)

validate_index2() (elsheeto.models.aviti.AvitiSample class method) value (elsheeto.models.aviti.AvitiSettingEntry attribute)

W

WARN_AND_PAD (elsheeto.parser.common.ColumnConsistency attribute) with_header_field_updated() (elsheeto.models.illumina_v1.IlluminaSampleSheet method) with_header_updated() (elsheeto.models.illumina_v1.IlluminaSampleSheet method) with_reads_updated() (elsheeto.models.illumina_v1.IlluminaSampleSheet method) with_run_value_added() (elsheeto.models.aviti.AvitiSheet method) with_run_values_updated() (elsheeto.models.aviti.AvitiSheet method) with_sample_added() (elsheeto.models.aviti.AvitiSheet method) (elsheeto.models.illumina_v1.IlluminaSampleSheet method) with_sample_modified() (elsheeto.models.aviti.AvitiSheet method) (elsheeto.models.illumina_v1.IlluminaSampleSheet method) with_sample_removed() (elsheeto.models.aviti.AvitiSheet method) (elsheeto.models.illumina_v1.IlluminaSampleSheet method)

with_samples_filtered() (elsheeto.models.aviti.AvitiSheet method) (elsheeto.models.illumina_v1.IlluminaSampleSheet method) with_setting_added() (elsheeto.models.aviti.AvitiSheet method) (elsheeto.models.illumina_v1.IlluminaSampleSheet method) with_settings_field_updated() (elsheeto.models.illumina_v1.IlluminaSampleSheet method) with_settings_updated() (elsheeto.models.illumina_v1.IlluminaSampleSheet method) workflow (elsheeto.models.illumina_v1.IlluminaHeader attribute) write_aviti_to_file() (in module elsheeto.facade) write_aviti_to_string() (in module elsheeto.facade) write_illumina_v1_to_file() (in module elsheeto.facade) write_illumina_v1_to_string() (in module elsheeto.facade)