Index

Symbols

--at pysec2pri-update-ids command line option pysec2pri-update-symbols command line option --datasource pysec2pri-diff command line option --datasources pysec2pri-all command line option --delac-file pysec2pri-uniprot command line option --entity-type pysec2pri-update-symbols command line option pysec2pri-wikidata-ids command line option pysec2pri-wikidata-symbols command line option --format pysec2pri-chebi-ids command line option pysec2pri-chebi-synonyms command line option pysec2pri-hgnc-ids command line option pysec2pri-hgnc-symbols command line option pysec2pri-hmdb command line option pysec2pri-ncbi-ids command line option pysec2pri-ncbi-symbols command line option pysec2pri-uniprot command line option pysec2pri-wikidata-ids command line option pysec2pri-wikidata-symbols command line option --mapping pysec2pri-update-ids command line option pysec2pri-update-symbols command line option --metabolites-file pysec2pri-hmdb command line option --metabolites-only pysec2pri-hmdb command line option --no-progress pysec2pri-update-ids command line option pysec2pri-update-symbols command line option --output pysec2pri-chebi-ids command line option pysec2pri-chebi-synonyms command line option pysec2pri-diff command line option pysec2pri-hgnc-ids command line option pysec2pri-hgnc-symbols command line option pysec2pri-hmdb command line option pysec2pri-ncbi-ids command line option pysec2pri-ncbi-symbols command line option pysec2pri-uniprot command line option pysec2pri-update-ids command line option pysec2pri-update-symbols command line option pysec2pri-wikidata-ids command line option pysec2pri-wikidata-symbols command line option --output-dir pysec2pri-all command line option

--proteins-file pysec2pri-hmdb command line option --proteins-only pysec2pri-hmdb command line option --sep pysec2pri-update-ids command line option pysec2pri-update-symbols command line option --show-all pysec2pri-diff command line option --subset pysec2pri-chebi-ids command line option pysec2pri-chebi-synonyms command line option pysec2pri-update-symbols command line option --suffix pysec2pri-update-ids command line option pysec2pri-update-symbols command line option --tax-id pysec2pri-ncbi-ids command line option pysec2pri-ncbi-symbols command line option pysec2pri-update-symbols command line option --test-subset pysec2pri-wikidata-ids command line option pysec2pri-wikidata-symbols command line option --version pysec2pri command line option pysec2pri-chebi-ids command line option pysec2pri-chebi-synonyms command line option pysec2pri-hgnc-ids command line option pysec2pri-hgnc-symbols command line option pysec2pri-hmdb command line option pysec2pri-ncbi-ids command line option pysec2pri-ncbi-symbols command line option pysec2pri-uniprot command line option pysec2pri-update-ids command line option pysec2pri-update-symbols command line option -o pysec2pri-all command line option pysec2pri-chebi-ids command line option pysec2pri-chebi-synonyms command line option pysec2pri-diff command line option pysec2pri-hgnc-ids command line option pysec2pri-hgnc-symbols command line option pysec2pri-hmdb command line option pysec2pri-ncbi-ids command line option pysec2pri-ncbi-symbols command line option pysec2pri-uniprot command line option pysec2pri-update-ids command line option pysec2pri-update-symbols command line option pysec2pri-wikidata-ids command line option pysec2pri-wikidata-symbols command line option

_

_primary_ids (Sec2PriMappingSet attribute)

A

added_count (MappingDiff property)

apply_metadata_to_mappingset() (BaseParser method)

B

BaseParser (class in pysec2pri.parsers.base)

build_lookup() (in module pysec2pri.update_ids) build_symbol_lookup() (in module pysec2pri.update_ids)

C

changed_count (MappingDiff property) ChEBIParser (class in pysec2pri.parsers.chebi) check_release() (in module pysec2pri.download) CloudflareBlockedError combine_mapping_sets() (in module pysec2pri.api) COMPLETE_SET_FILE pysec2pri-hgnc-symbols command line option

complete_set_source_url (HGNCParser property) compute_cardinalities() (IdMappingSet method) (LabelMappingSet method) config (BaseParser property) create_mapping_set() (BaseParser method)

D

DATASOURCE pysec2pri-update-ids command line option pysec2pri-update-symbols command line option DatasourceConfig (class in pysec2pri.parsers.base)

delac_url (UniProtParser property) diff_mapping_sets() (in module pysec2pri.diff) diff_sssom_files() (in module pysec2pri.diff) download_datasource() (in module pysec2pri.download) download_file() (in module pysec2pri.download)

F

FILE1 pysec2pri-diff command line option

FILE2 pysec2pri-diff command line option

G

generate_chebi() (in module pysec2pri.api) generate_chebi_synonyms() (in module pysec2pri.api) generate_hgnc() (in module pysec2pri.api) generate_hgnc_primary_ids() (in module pysec2pri.api) generate_hgnc_symbols() (in module pysec2pri.api) generate_hmdb() (in module pysec2pri.api) generate_hmdb_proteins() (in module pysec2pri.api) generate_ncbi() (in module pysec2pri.api) generate_ncbi_symbols() (in module pysec2pri.api)

generate_uniprot() (in module pysec2pri.api) generate_wikidata() (in module pysec2pri.api) generate_wikidata_symbols() (in module pysec2pri.api) get_curie_map() (BaseParser method) get_download_url() (BaseParser method) get_download_urls() (in module pysec2pri.download) get_latest_release_info() (in module pysec2pri.download) get_mapping_metadata() (BaseParser method) get_mappingset_metadata() (BaseParser method)

H

has_changes (MappingDiff property) HGNCParser (class in pysec2pri.parsers.hgnc)

history_source_url (NCBIParser property) HMDBParser (class in pysec2pri.parsers.hmdb)

I

IdMappingSet (class in pysec2pri.parsers.base) info_source_url (NCBIParser property) INPUT_FILE pysec2pri-chebi-ids command line option pysec2pri-chebi-synonyms command line option pysec2pri-hgnc-ids command line option pysec2pri-ncbi-ids command line option pysec2pri-ncbi-symbols command line option pysec2pri-uniprot command line option pysec2pri-update-ids command line option pysec2pri-update-symbols command line option pysec2pri-wikidata-ids command line option pysec2pri-wikidata-symbols command line option

intersection_count (MappingDiff property) is_withdrawn() (BaseParser static method) is_withdrawn_primary() (BaseParser static method)

L

LabelMappingSet (class in pysec2pri.parsers.base) load_label_mapping() (in module pysec2pri.api)

load_mapping() (in module pysec2pri.api) load_metadata() (BaseParser method)

M

MappingDiff (class in pysec2pri.diff) module pysec2pri.api pysec2pri.constants pysec2pri.diff pysec2pri.download pysec2pri.exports pysec2pri.update_ids

N

NCBIParser (class in pysec2pri.parsers.ncbi)

normalize_withdrawn_id() (BaseParser static method)

P

parse() (BaseParser method) (ChEBIParser method) (HGNCParser method) (HMDBParser method) (NCBIParser method) (UniProtParser method) (WikidataParser method) parse_all() (HGNCParser method) (NCBIParser method) (WikidataParser method) parse_from_file() (WikidataParser method) parse_primary_ids() (HGNCParser method) parse_proteins() (HMDBParser method) parse_symbols() (HGNCParser method) (NCBIParser method) (WikidataParser method) parse_synonyms() (ChEBIParser method) pysec2pri command line option --version pysec2pri-all command line option --datasources --output-dir -o pysec2pri-chebi-ids command line option --format --output --subset --version -o INPUT_FILE pysec2pri-chebi-synonyms command line option --format --output --subset --version -o INPUT_FILE pysec2pri-diff command line option --datasource --output --show-all -o FILE1 FILE2 pysec2pri-hgnc-ids command line option --format --output --version -o INPUT_FILE pysec2pri-hgnc-symbols command line option --format --output --version -o COMPLETE_SET_FILE pysec2pri-hmdb command line option --format --metabolites-file --metabolites-only --output --proteins-file --proteins-only --version -o pysec2pri-ncbi-ids command line option --format --output --tax-id --version -o INPUT_FILE

pysec2pri-ncbi-symbols command line option --format --output --tax-id --version -o INPUT_FILE pysec2pri-uniprot command line option --delac-file --format --output --version -o INPUT_FILE pysec2pri-update-ids command line option --at --mapping --no-progress --output --sep --suffix --version -o DATASOURCE INPUT_FILE pysec2pri-update-symbols command line option --at --entity-type --mapping --no-progress --output --sep --subset --suffix --tax-id --version -o DATASOURCE INPUT_FILE pysec2pri-wikidata-ids command line option --entity-type --format --output --test-subset -o INPUT_FILE pysec2pri-wikidata-symbols command line option --entity-type --format --output --test-subset -o INPUT_FILE pysec2pri.api module pysec2pri.constants module pysec2pri.diff module pysec2pri.download module pysec2pri.exports module pysec2pri.update_ids module

R

ReleaseInfo (class in pysec2pri.download) removed_count (MappingDiff property)

resolve_ids() (in module pysec2pri.api) resolve_symbols() (in module pysec2pri.api)

S

save() (IdMappingSet method) (in module pysec2pri.api) (LabelMappingSet method) (Sec2PriMappingSet method)

Sec2PriMappingSet (class in pysec2pri.parsers.base) sec_ac_url (UniProtParser property) source_url (ChEBIParser property) (HMDBParser property) summarize_diff() (in module pysec2pri.diff)

T

to_json() (Sec2PriMappingSet method) to_name2synonym() (LabelMappingSet method) to_owl() (Sec2PriMappingSet method) to_pri_ids() (IdMappingSet method) to_pri_symbols() (LabelMappingSet method)

to_rdf() (Sec2PriMappingSet method) to_sec2pri() (IdMappingSet method) to_sssom() (Sec2PriMappingSet method) to_symbol_sec2pri() (LabelMappingSet method) total_changes (MappingDiff property)

U

UniProtParser (class in pysec2pri.parsers.uniprot)

update_ids() (in module pysec2pri.update_ids) update_symbols() (in module pysec2pri.update_ids)

W

WikidataParser (class in pysec2pri.parsers.wikidata) withdrawn_source_url (HGNCParser property) write_all_formats() (in module pysec2pri.api) write_diff_output() (in module pysec2pri.api) write_json() (in module pysec2pri.api) (in module pysec2pri.exports) write_name2synonym() (in module pysec2pri.api) (in module pysec2pri.exports) write_output() (in module pysec2pri.api) (in module pysec2pri.exports) write_owl() (in module pysec2pri.api) (in module pysec2pri.exports)

write_pri_ids() (in module pysec2pri.exports) write_rdf() (in module pysec2pri.api) (in module pysec2pri.exports) write_sec2pri() (in module pysec2pri.api) (in module pysec2pri.exports) write_secondary() (in module pysec2pri.exports) write_sssom() (in module pysec2pri.api) (in module pysec2pri.exports) write_symbol2prev() (in module pysec2pri.exports) write_symbol_sec2pri() (in module pysec2pri.api)