Handling data from UniProt

This module provides functionalities for fetching and processing protein information from the UniProt database.

Functions:

  • fetch_uniprot_info(accession_id): Fetches information for a given protein accession code from the UniProt database.

  • fetch_uniprot_domains(protein): Identifies and returns the domains of a protein based on the fetched UniProt data

Dependencies:

  • requests: Required for making HTTP requests to the UniProt API.

  • .classes: Contains the Domain class used to represent protein domains.

alphafragment.uniprot_fetch.fetch_uniprot_info(accession_id)

Fetches and returns protein information from the UniProt database for a given accession code.

Parameters:

  • accession_id (str): The accession id of the protein for which to fetch domain information. If ‘na’ or a similar placeholder is provided, the function will not attempt a request and will return None immediately.

Returns:

  • dict or None: The JSON response as a dictionary if the request is successful; otherwise, None.

Errors and Exceptions:

  • If the HTTP request fails due to reasons such as an invalid accession code or network issues, an error message is printed, and the function returns None.

  • If exceptions occur during the request or while parsing the JSON response (eg timeouts, connection errors, or issues with the format of the received data), an error message is printed, and the function returns None.

Note:

  • This function requires the requests library to make HTTP requests.

  • A timeout is set to 30 seconds for the HTTP request to prevent hanging.

alphafragment.uniprot_fetch.find_uniprot_domains(protein)

Extracts domain information for a given protein from UniProt data.

Parameters:

  • protein (Protein): The protein object for which domain information is to be fetched. The object should have a valid ‘accession_id’ attribute that corresponds to its UniProt accession code.

Returns:

  • list of Domain objects: A list containing Domain objects for each domain found in the UniProt data. Domain positions are given using Pythonic 0-based indexing, so will be 1 less than the UniProt positions.

Errors and Exceptions:

  • If no data can be retrieved from UniProt for by the fetch_uniprot_info function returns None, this function prints a message and returns None.

  • If the start or end positions of a domain cannot be converted to integers, a ValueError will be raised.

Notes:

  • The function intentionally excludes domains of types ‘CHAIN’, ‘MUTAGEN’, ‘CONFLICT’, ‘VARIANT’, ‘VAR_SEQ’ and ‘CROSSLNK’. This is because: - CHAIN types cover the entire sequence and do not represent discrete structural

    domains, making them unsuitable for analyses that require domain fragmentation.

    • MUTAGEN, CONFLICT, VARIANT, VAR_SEQ and CROSSLNK types are not considered structurally relevant domains for the purpose of protein analysis and domain identification.

  • In specific cases where it is necessary to include these excluded domain types, or to specify domains not found or incorrectly annotated in UniProt, users can manually specify domains in the input CSV file used with other functions of this module.

  • Domains are identified by their UniProt description - if no description is available, the function will attempt to use the ‘type’ field.