uniprot-id-mapping 2024.1

A collection of recurring mixin classes.

---

title: README

Synopsis

A wrapper around the UniProt ID Mapping web service with local caching to speed up subsequent queries and reduce server load. The package provides both a Python library and a command-line utility for mapping IDs between any of the supported databases.

Links

GitLab

• Homepage
• Source
• Documentation
• Issues
• GitLab package registry

Usage

Python API

# Import the IdMapper class.
from uniprot_id_mapping import IdMapper

# Instantiate it.
id_mapper = IdMapper()

# Create a list or other iterable of IDs.
ids = ["P21802", "P12345"]

# Get a dict mapping the given IDs from UniProtKB_AC-ID to UniRef90.
mapped = id_mapper.map_ids("UniProtKB_AC-ID", "UniRef90", ids)

# Get the JSON object containing the information about available fields.
fields = id_mapper.fields

For further details, please see the API documentation linked above.

Command-Line Utility

The package installs the command-line utillity uniprot-id_mapper which can be used to map IDs from command-line arguments or input files. The results can be printed in plain test or as JSON. The utility also provides subcommands for managing the cached results and listing available databases.

usage: uniprot-id_mapper [-h] [--cache-dir CACHE_DIR] [-j] [-t TIMEOUT] [-v]
                         {map,list,clear} ...

Map IDs between databases using UniProt's ID Mapping service.

positional arguments:
  {map,list,clear}
    map                 Map given IDs from one database to another
    list                List available "from" and "to" databases.
    clear               Clear the cache. If you only wish to clear missing
                        identifiers, use the --clear-missing option of the
                        "map" command.

options:
  -h, --help            show this help message and exit
  --cache-dir CACHE_DIR
                        A directory for caching results locally. If not given,
                        a standard path will be used.
  -j, --json            Output results in JSON.
  -t TIMEOUT, --timeout TIMEOUT
                        Timeout for establishing remote connections.
  -v, --verbose         Increase logging level to DEBUG.

Map

usage: uniprot-id_mapper map [-h] [--id-list ID_LIST] [--refresh-missing]
                             from to [id ...]

positional arguments:
  from               The database of the given IDs.
  to                 The target database to which to map the given IDs.
  id                 The IDs to map.

options:
  -h, --help         show this help message and exit
  --id-list ID_LIST  Path to a file with a list of IDs, one per line.
  --refresh-missing  Query the server for previously missing identifiers
                     instead of using cached values.

List

Help Message

usage: uniprot-id_mapper list [-h]

options:
  -h, --help  show this help message and exit

Example Output

From
  Allergome
  ArachnoServer
  Araport
  BioCyc
  BioGRID
  BioMuta
  CCDS
  CGD
  CPTAC
  CRC64
  ChEMBL
  ChiTaRS
  CollecTF
  ComplexPortal
  ConoServer
  DIP
  DMDM
  DNASU
  DisProt
  DrugBank
  EMBL-GenBank-DDBJ
  EMBL-GenBank-DDBJ_CDS
  ESTHER
  EchoBASE
  Ensembl
  Ensembl_Genomes
  Ensembl_Genomes_Protein
  Ensembl_Genomes_Transcript
  Ensembl_Protein
  Ensembl_Transcript
  FlyBase
  GI_number
  GeneCards
  GeneID
  GeneReviews
  GeneTree
  GeneWiki
  Gene_Name
  GenomeRNAi
  GlyConnect
  GuidetoPHARMACOLOGY
  HGNC
  HOGENOM
  IDEAL
  KEGG
  LegioList
  Leproma
  MEROPS
  MGI
  MIM
  MaizeGDB
  OMA
  OpenTargets
  Orphanet
  OrthoDB
  PATRIC
  PDB
  PHI-base
  PIR
  PeroxiBase
  PharmGKB
  PlantReactome
  PomBase
  ProteomicsDB
  PseudoCAP
  REBASE
  RGD
  Reactome
  RefSeq_Nucleotide
  RefSeq_Protein
  SGD
  STRING
  SwissLipids
  TCDB
  TreeFam
  TubercuList
  UCSC
  UniParc
  UniPathway
  UniProtKB_AC-ID
  UniRef100
  UniRef50
  UniRef90
  VEuPathDB
  VGNC
  WBParaSite
  WBParaSite_Transcript-Protein
  WormBase
  WormBase_Protein
  WormBase_Transcript
  Xenbase
  ZFIN
  dictyBase
  eggNOG
  euHCVdb
  neXtProt

To
  Allergome
  ArachnoServer
  Araport
  BioCyc
  BioGRID
  BioMuta
  CCDS
  CGD
  CPTAC
  CRC64
  ChEMBL
  ChiTaRS
  CollecTF
  ComplexPortal
  ConoServer
  DIP
  DMDM
  DNASU
  DisProt
  DrugBank
  EMBL-GenBank-DDBJ
  EMBL-GenBank-DDBJ_CDS
  ESTHER
  EchoBASE
  Ensembl
  Ensembl_Genomes
  Ensembl_Genomes_Protein
  Ensembl_Genomes_Transcript
  Ensembl_Protein
  Ensembl_Transcript
  FlyBase
  GI_number
  GeneCards
  GeneID
  GeneReviews
  GeneTree
  GeneWiki
  Gene_Name
  GenomeRNAi
  GlyConnect
  GuidetoPHARMACOLOGY
  HGNC
  HOGENOM
  IDEAL
  KEGG
  LegioList
  Leproma
  MEROPS
  MGI
  MIM
  MaizeGDB
  OMA
  OpenTargets
  Orphanet
  OrthoDB
  PATRIC
  PDB
  PHI-base
  PIR
  PeroxiBase
  PharmGKB
  PlantReactome
  PomBase
  ProteomicsDB
  PseudoCAP
  REBASE
  RGD
  Reactome
  RefSeq_Nucleotide
  RefSeq_Protein
  SGD
  STRING
  SwissLipids
  TCDB
  TreeFam
  TubercuList
  UCSC
  UniParc
  UniPathway
  UniProtKB
  UniProtKB-Swiss-Prot
  UniRef100
  UniRef50
  UniRef90
  VEuPathDB
  VGNC
  WBParaSite
  WBParaSite_Transcript-Protein
  WormBase
  WormBase_Protein
  WormBase_Transcript
  Xenbase
  ZFIN
  dictyBase
  eggNOG
  euHCVdb
  neXtProt

Clear

usage: uniprot-id_mapper clear [-h]

options:
  -h, --help  show this help message and exit