spirepy.study¶

Classes¶

Study

A study from SPIRE.

Module Contents¶

class spirepy.study.Study(name: str)[source]¶

A study from SPIRE.

This class represents a study from the SPIRE database. It automatically fetches metadata and automates the initialization of samples to further use to obtain its genomic, geographical or other types of data provided by it.

Parameters:: name (str) – Internal ID for the study.

name[source]¶

get_metadata() → polars.DataFrame[source]¶

Retrieve metadata for the study.

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

get_samples() → list[source]¶

Retrive a list of samples for the study.

Returns:: List of spirepy.sample.Sample that belong to the study.
Return type:: list

get_mags() → polars.DataFrame[source]¶

Get a DataFrame with information regarding the MAGs.

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

download_assemblies(output: str)[source]¶

Download the assemblies into a specified folder.

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

download_mags(output: str)[source]¶

Download the MAGs into a specified folder.

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

download_genecalls(output: str)[source]¶

Download the genecalls into a specified folder.

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

download_proteins(output: str)[source]¶

Download the proteins into a specified folder.

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