freqsap.uniprot
===============

.. py:module:: freqsap.uniprot

.. autoapi-nested-parse::

   Module for interacting with the UniProt API.



Classes
-------

.. autoapisummary::

   freqsap.uniprot.UniProt


Module Contents
---------------

.. py:class:: UniProt(timeout: int = 3)

   Bases: :py:obj:`freqsap.interfaces.ProteinVariantAPI`


   Interface to the UniProt protein database API.

   Provides methods to query protein information and variations from UniProt.


   .. py:attribute:: _params


   .. py:attribute:: _headers


   .. py:attribute:: _timeout
      :value: 3



   .. py:method:: get(accession: freqsap.accession.Accession) -> freqsap.protein.Protein

      Retrieve protein and its variations from UniProt.

      :param accession: The protein accession identifier.
      :type accession: Accession

      :returns: The protein object with its variations.
      :rtype: Protein



   .. py:method:: query(accession: str) -> dict

      Query UniProt for protein data.

      :param accession: The protein accession identifier.
      :type accession: str

      :returns: JSON response from UniProt API.
      :rtype: dict

      :raises requests.HTTPError: If the request fails.



   .. py:method:: parse(feature: dict) -> freqsap.variation.Variation | None

      Parse a feature dictionary to extract variation information.

      :param feature: Feature dictionary from UniProt response.
      :type feature: dict

      :returns: Variation object if a valid dbSNP reference is found, None otherwise.
      :rtype: Variation | None



   .. py:method:: request(url: str) -> requests.Response

      Make an HTTP GET request to UniProt.

      :param url: The URL to request.
      :type url: str

      :returns: The HTTP response.
      :rtype: requests.Response



   .. py:method:: is_dbsnp(xref: dict) -> bool

      Check if a cross-reference is a dbSNP reference.

      :param xref: Cross-reference dictionary.
      :type xref: dict

      :returns: True if the reference is from dbSNP and starts with 'rs', False otherwise.
      :rtype: bool



   .. py:method:: available() -> bool

      Check if the UniProt API is available.

      :returns: True if the service is available, False otherwise.
      :rtype: bool