freqsap.ebi
===========

.. py:module:: freqsap.ebi

.. autoapi-nested-parse::

   Module for interacting with the EBI Proteins API.



Classes
-------

.. autoapisummary::

   freqsap.ebi.EBI


Functions
---------

.. autoapisummary::

   freqsap.ebi._get_dbsnp_id
   freqsap.ebi._check_response
   freqsap.ebi._get_variants


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

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

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


   Class to access the EBI protein API.


   .. py:attribute:: _headers


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



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

      Private function to submit requests.

      :param url: Base URL to query.
      :type url: str

      :returns: Response returned by the server.
      :rtype: requests.Response



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

      Check whether the service is available.

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



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

      Get the protein represented by the Accession.

      :param accession: Accession of the Protein.
      :type accession: Accession

      :returns: Protein specified by the accession.
      :rtype: Protein



.. py:function:: _get_dbsnp_id(xrefs: list[dict]) -> str | None

   Parse dbSNP id from the xrefs entry. Private function.

   :param xrefs: List of xrefs specified in the protein.
   :type xrefs: list[dict]

   :returns: dbSNP id, if found, otherwise None.
   :rtype: str | None


.. py:function:: _check_response(accession: freqsap.accession.Accession, response: requests.Response) -> None

   Check the response for the accession for errors.

   :param accession: Accession which was searched.
   :type accession: Accession
   :param response: Response obtained from the server.
   :type response: requests.Response

   :raises AccessionNotFound: Raises exception if the accession wasn't found.
   :raises Raises all other exceptions raised by the requests module.:


.. py:function:: _get_variants(response: dict) -> Generator[freqsap.variation.Variation]

   Extract variations from EBI API response.

   :param response: JSON response from EBI API containing protein features.
   :type response: dict

   :Yields: *Variation* -- Each variation found with a valid dbSNP reference ID.