UniProt client

protmapper.uniprot_client.get_chains(protein_id)

Return the list of cleaved chains for the given protein.

Parameters:protein_id (str) – The UniProt ID of the protein whose cleaved chains are to be returned. Returns:A list of Feature named tuples representing each chain. Return type:list of Feature

protmapper.uniprot_client.get_entrez_id(protein_id)

Return the Entrez ID given a protein ID.

Parameters:protein_id (str) – UniProt ID of the protein Returns:Entrez ID of the corresponding gene or None if not available. Return type:str or None

protmapper.uniprot_client.get_family_members(family_name, human_only=True)

Return the HGNC gene symbols which are the members of a given family.

Parameters:

• family_name (str) – Family name to be queried.
• human_only (bool) – If True, only human proteins in the family will be returned. Default: True

Returns:

gene_names – The HGNC gene symbols corresponding to the given family.

Return type:

list

protmapper.uniprot_client.get_feature_by_id(feature_id)

Return a Feature based on its unique feature ID.

Parameters:feature_id (str) – A Feature ID, of the form PRO_*. Returns:A Feature with the given ID. Return type:Feature or None

protmapper.uniprot_client.get_feature_of(feature_id)

Return the UniProt ID of the protein to which the given feature belongs.

Parameters:feature_id (str) – A Feature ID, of the form PRO_*. Returns:A UniProt ID corresponding to the given feature, or None if not available (generally shouldn’t happen, unless the feature ID is invalid). Return type:str or None

protmapper.uniprot_client.get_features(protein_id)

Return a list of features (chains, peptides) for a given protein.

Parameters:protein_id (str) – The UniProt ID of the protein whose features are to be returned. Returns:A list of Feature named tuples representing each Feature. Return type:list of Feature

protmapper.uniprot_client.get_function(protein_id)

Return the function description of a given protein.

Parameters:protein_id (str) – The UniProt ID of the protein. Returns:The function description of the protein. Return type:str

protmapper.uniprot_client.get_gene_name(protein_id, web_fallback=True)

Return the gene name or canonical protein name for the given UniProt ID.

If available, this function returns the primary gene name provided by UniProt. If not available, the primary protein name is returned.

Parameters:

• protein_id (str) – UniProt ID to be mapped.
• web_fallback (Optional[bool]) – If True and the offline lookup fails, the UniProt web service is used to do the query.

Returns:

gene_name – The gene name corresponding to the given Uniprot ID.

Return type:

str

protmapper.uniprot_client.get_gene_synonyms(protein_id: str) → List[str]

Return a list of synonyms for the gene corresponding to a protein.

Note that synonyms here also include the official gene name as returned by get_gene_name.

Parameters:protein_id – The UniProt ID of the protein to query Returns:The list of synonyms of the gene corresponding to the protein

protmapper.uniprot_client.get_hgnc_id(protein_id)

Return the HGNC ID given the protein id of a human protein.

Parameters:protein_id (str) – UniProt ID of the human protein Returns:hgnc_id – HGNC ID of the human protein Return type:str

protmapper.uniprot_client.get_id_from_entrez(entrez_id)

Return the UniProt ID given the Entrez ID of a gene.

Parameters:entrez_id (str) – Entrez ID of the gene Returns:UniProt ID of the corresponding protein or None if not available. Return type:str or None

protmapper.uniprot_client.get_id_from_mgi(mgi_id)

Return the UniProt ID given the MGI ID of a mouse protein.

Parameters:mgi_id (str) – The MGI ID of the mouse protein. Returns:up_id – The UniProt ID of the mouse protein. Return type:str

protmapper.uniprot_client.get_id_from_mgi_name(mgi_name: str) → Optional[str]

Return the UniProt ID given the MGI name of a mouse protein.

Parameters:mgi_name (str) – The MGI name of the mouse protein. Returns:up_id – The UniProt ID of the mouse protein. Return type:str

protmapper.uniprot_client.get_id_from_mnemonic(uniprot_mnemonic)

Return the UniProt ID for the given UniProt mnemonic.

Parameters:uniprot_mnemonic (str) – UniProt mnemonic to be mapped. Returns:uniprot_id – The UniProt ID corresponding to the given Uniprot mnemonic. Return type:str

protmapper.uniprot_client.get_id_from_rgd(rgd_id)

Return the UniProt ID given the RGD ID of a rat protein.

Parameters:rgd_id (str) – The RGD ID of the rat protein. Returns:up_id – The UniProt ID of the rat protein. Return type:str

protmapper.uniprot_client.get_id_from_rgd_name(rgd_name: str) → Optional[str]

Return the UniProt ID given the RGD name of a rat protein.

Parameters:rgd_name (str) – The RGD name of the rat protein. Returns:up_id – The UniProt ID of the rat protein. Return type:str

protmapper.uniprot_client.get_ids_from_refseq(refseq_id, reviewed_only=False)

Return UniProt IDs from a RefSeq ID”.

Parameters:

• refseq_id (str) – The RefSeq ID of the protein to map.
• reviewed_only (Optional[bool]) – If True, only reviewed UniProt IDs are returned. Default: False

Returns:

A list of UniProt IDs corresponding to the RefSeq ID.

Return type:

list of str

protmapper.uniprot_client.get_length(protein_id)

Return the length (number of amino acids) of a protein.

Parameters:protein_id (str) – UniProt ID of a protein. Returns:length – The length of the protein in amino acids. Return type:int

protmapper.uniprot_client.get_mgi_id(protein_id)

Return the MGI ID given the protein id of a mouse protein.

Parameters:protein_id (str) – UniProt ID of the mouse protein Returns:mgi_id – MGI ID of the mouse protein Return type:str

protmapper.uniprot_client.get_mnemonic(protein_id, web_fallback=False)

Return the UniProt mnemonic for the given UniProt ID.

Parameters:

• protein_id (str) – UniProt ID to be mapped.
• web_fallback (Optional[bool]) – If True and the offline lookup fails, the UniProt web service is used to do the query.

Returns:

mnemonic – The UniProt mnemonic corresponding to the given Uniprot ID.

Return type:

str

protmapper.uniprot_client.get_modifications(protein_id: str) → List[Tuple[str, int]]

Return a list of modifications for a protein.

Parameters:protein_id – The UniProt ID of the protein to query Returns:The list of modifications of the protein, each represented as a tuple of residue description string and position string.

protmapper.uniprot_client.get_mouse_id(human_protein_id)

Return the mouse UniProt ID given a human UniProt ID.

Parameters:human_protein_id (str) – The UniProt ID of a human protein. Returns:mouse_protein_id – The UniProt ID of a mouse protein orthologous to the given human protein. Return type:str

protmapper.uniprot_client.get_organism_id(protein_id)

Return the Taxonomy ID of the organism that a protein belongs to.

Parameters:protein_id (str) – The UniProt ID of a protein. Returns:The Taxonomy ID of the organism the protein belongs to or None if not available. Return type:str or None

protmapper.uniprot_client.get_primary_id(protein_id)

Return a primary entry corresponding to the UniProt ID.

Parameters:protein_id (str) – The UniProt ID to map to primary. Returns:primary_id – If the given ID is primary, it is returned as is. Otherwise the primary IDs are looked up. If there are multiple primary IDs then the first human one is returned. If there are no human primary IDs then the first primary found is returned. Return type:str

protmapper.uniprot_client.get_protein_synonyms(protein_id)

Return a list of synonyms for a protein.

Note that this function returns protein synonyms as provided by UniProt. The get_gene_synonym returns synonyms given for the gene corresponding to the protein, and get_synonyms returns both.

Parameters:protein_id (str) – The UniProt ID of the protein to query Returns:synonyms – The list of synonyms of the protein Return type:list[str]

protmapper.uniprot_client.get_rat_id(human_protein_id)

Return the rat UniProt ID given a human UniProt ID.

Parameters:human_protein_id (str) – The UniProt ID of a human protein. Returns:rat_protein_id – The UniProt ID of a rat protein orthologous to the given human protein Return type:str

protmapper.uniprot_client.get_rgd_id(protein_id)

Return the RGD ID given the protein id of a rat protein.

Parameters:protein_id (str) – UniProt ID of the rat protein Returns:rgd_id – RGD ID of the rat protein Return type:str

protmapper.uniprot_client.get_signal_peptide(protein_id, web_fallback=True)

Return the position of a signal peptide for the given protein.

Parameters:

• protein_id (str) – The UniProt ID of the protein whose signal peptide position is to be returned.
• web_fallback (Optional[bool]) – If True the UniProt web service is used to download information when the local resource file doesn’t contain the right information.

Returns:

A Feature named tuple representing the signal peptide.

Return type:

Feature

protmapper.uniprot_client.get_synonyms(protein_id)

Return synonyms for a protein and its associated gene.

Parameters:protein_id (str) – The UniProt ID of the protein to query Returns:synonyms – The list of synonyms of the protein and its associated gene. Return type:list[str]

protmapper.uniprot_client.is_human(protein_id)

Return True if the given protein id corresponds to a human protein.

Parameters:protein_id (str) – UniProt ID of the protein Returns: Return type:True if the protein_id corresponds to a human protein, otherwise False.

protmapper.uniprot_client.is_mouse(protein_id)

Return True if the given protein id corresponds to a mouse protein.

Parameters:protein_id (str) – UniProt ID of the protein Returns: Return type:True if the protein_id corresponds to a mouse protein, otherwise False.

protmapper.uniprot_client.is_rat(protein_id)

Return True if the given protein id corresponds to a rat protein.

Parameters:protein_id (str) – UniProt ID of the protein Returns: Return type:True if the protein_id corresponds to a rat protein, otherwise False.

protmapper.uniprot_client.is_reviewed(protein_id)

Return True if the UniProt ID corresponds to a reviewed entry.

Parameters:protein_id (str) – The UniProt ID to check. Returns: Return type:True if it is a reviewed entry, False otherwise.

protmapper.uniprot_client.is_secondary(protein_id)

Return True if the UniProt ID corresponds to a secondary accession.

Parameters:protein_id (str) – The UniProt ID to check. Returns: Return type:True if it is a secondary accessing entry, False otherwise.

protmapper.uniprot_client.query_protein

Retrieve the XML entry for a given protein.

Parameters:protein_id – The UniProt ID of the protein to look up. Returns:An ElementTree representation of the XML entry for the protein.

protmapper.uniprot_client.verify_location(protein_id, residue, location)

Return True if the residue is at the given location in the UP sequence.

Parameters:

• protein_id (str) – UniProt ID of the protein whose sequence is used as reference.
• residue (str) – A single character amino acid symbol (Y, S, T, V, etc.)
• location (str) – The location on the protein sequence (starting at 1) at which the residue should be checked against the reference sequence.

Returns:

• True if the given residue is at the given position in the sequence
• corresponding to the given UniProt ID, otherwise False.

protmapper.uniprot_client.verify_modification(protein_id, residue, location=None)

Return True if the residue at the given location has a known modifiation.

Parameters:

• protein_id (str) – UniProt ID of the protein whose sequence is used as reference.
• residue (str) – A single character amino acid symbol (Y, S, T, V, etc.)
• location (Optional[str]) – The location on the protein sequence (starting at 1) at which the modification is checked.

Returns:

• True if the given residue is reported to be modified at the given position
• in the sequence corresponding to the given UniProt ID, otherwise False.
• If location is not given, we only check if there is any residue of the
• given type that is modified.