spirepy.sample
==============

.. py:module:: spirepy.sample


Classes
-------

.. autoapisummary::

   spirepy.sample.Sample


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

.. py:class:: Sample(id: str, study: spirepy.study.Study = None)

   A sample from SPIRE.

   This class represents a sample from the SPIRE database. It is designed to
   provide all the properties and methods to allow work with samples and
   provide tools for automation and scalability.

   :param id: Internal ID for the sample.
   :type id: str

   :param study: The :class:`spirepy.study.Study` to which the sample belongs to, defaults to :class:`None`.
   :type study: :class:`spirepy.study.Study`, optional


   .. py:attribute:: id


   .. py:attribute:: study
      :value: None



   .. py:method:: get_metadata() -> polars.DataFrame

      Retrieve the metadata for a sample.

      :return: A Dataframe with the sample's metadata.
      :rtype: :class:`polars.DataFrame`



   .. py:method:: get_mags() -> polars.DataFrame

      Retrieve the MAGs for a sample.

      :return: A Dataframe with the sample's MAGs.
      :rtype: :class:`polars.DataFrame`



   .. py:method:: get_eggnog_data() -> polars.DataFrame

      Retrive the EggNOG-mapper data for a sample.

      :return: A Dataframe with the sample's EggNOG-mapper data.
      :rtype: :class:`polars.DataFrame`



   .. py:method:: get_amr_annotations(mode: str = 'deeparg') -> Union[None, polars.DataFrame]

      Obtain the anti-microbial resistance annotations for the sample.

      :param mode: Tool to select the AMR data from. Options are deepARG (deeparg), abricate-megares (megares) and abricate-vfdb (vfdb); defaults to deepARG.
      :type mode: str, optional

      :return: A Dataframe with the sample's AMR data.
      :rtype: :class:`polars.DataFrame`



   .. py:method:: get_contig_depths() -> polars.DataFrame

      Obtain the contig depth data for the sample.

      :return: A Dataframe with the sample's contig depth data.
      :rtype: :class:`polars.DataFrame`



   .. py:method:: download_mags(out_folder: str)

      Download the MAGs into a specified folder.

      :param output: Output folder to download the MAGs to.
      :type output: str