spirepy.sample¶

Classes¶

Sample

A sample from SPIRE.

Module Contents¶

class spirepy.sample.Sample(id: str, study: spirepy.study.Study = None)[source]¶

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.

Parameters:

id (str) – Internal ID for the sample.
study (spirepy.study.Study, optional) – The spirepy.study.Study to which the sample belongs to, defaults to None.

id[source]¶

study = None[source]¶

get_metadata() → polars.DataFrame[source]¶

Retrieve the metadata for a sample.

Returns:: A Dataframe with the sample’s metadata.
Return type:: polars.DataFrame

get_mags() → polars.DataFrame[source]¶

Retrieve the MAGs for a sample.

Returns:: A Dataframe with the sample’s MAGs.
Return type:: polars.DataFrame

get_eggnog_data() → polars.DataFrame[source]¶

Retrive the EggNOG-mapper data for a sample.

Returns:: A Dataframe with the sample’s EggNOG-mapper data.
Return type:: polars.DataFrame

get_amr_annotations(mode: str = 'deeparg') → None | polars.DataFrame[source]¶

Obtain the anti-microbial resistance annotations for the sample.

Parameters:: mode (str, optional) – Tool to select the AMR data from. Options are deepARG (deeparg), abricate-megares (megares) and abricate-vfdb (vfdb); defaults to deepARG.
Returns:: A Dataframe with the sample’s AMR data.
Return type:: polars.DataFrame

get_contig_depths() → polars.DataFrame[source]¶

Obtain the contig depth data for the sample.

Returns:: A Dataframe with the sample’s contig depth data.
Return type:: polars.DataFrame

download_mags(out_folder: str)[source]¶

Download the MAGs into a specified folder.

Parameters:: output (str) – Output folder to download the MAGs to.