dolomite_se package

Submodules

dolomite_se.read_ranged_summarized_experiment module

dolomite_se.read_ranged_summarized_experiment.read_ranged_summarized_experiment(path, metadata, **kwargs)[source]

Load a RangedSummarizedExperiment from its on-disk representation.

This method should generally not be called directly but instead be invoked by read_object().

Parameters:

  • path (str) – Path to the directory containing the object.

  • metadata (dict) – Metadata for the object.

  • kwargs – Further arguments.

Return type:

RangedSummarizedExperiment

Returns:

A RangedSummarizedExperiment with file-backed arrays in the assays.

dolomite_se.read_summarized_experiment module

dolomite_se.read_summarized_experiment.read_summarized_experiment(path, metadata, **kwargs)[source]

Load a SummarizedExperiment from its on-disk representation.

This method should generally not be called directly but instead be invoked by read_object().

Parameters:

  • path (str) – Path to the directory containing the object.

  • metadata (dict) – Metadata for the object.

  • kwargs – Further arguments.

Return type:

SummarizedExperiment

Returns:

A SummarizedExperiment with file-backed arrays in the assays.

dolomite_se.save_ranged_summarized_experiment module

dolomite_se.save_ranged_summarized_experiment.save_ranged_summarized_experiment(x, path, data_frame_args=None, assay_args=None, **kwargs)[source]

Method for saving SummarizedExperiment objects to their corresponding file representations, see save_object() for details.

Parameters:

  • x (RangedSummarizedExperiment) – Object to be staged.

  • path (str) – Path to a directory in which to save x.

  • data_frame_args (dict) – Further arguments to pass to the save_object method for the row/column data.

  • assay_args (dict) – Further arguments to pass to the save_object method for the assays.

  • kwargs – Further arguments.

Returns:

x is saved to path.

dolomite_se.save_summarized_experiment module

dolomite_se.save_summarized_experiment.save_summarized_experiment(x, path, data_frame_args=None, assay_args=None, **kwargs)[source]

Method for saving SummarizedExperiment objects to their corresponding file representations, see save_object() for details.

Parameters:

  • x (SummarizedExperiment) – Object to be staged.

  • path (str) – Path to a directory in which to save x.

  • data_frame_args (dict) – Further arguments to pass to the save_object method for the row/column data.

  • assay_args (dict) – Further arguments to pass to the save_object method for the assays.

  • kwargs – Further arguments.

Returns:

x is saved to path.

dolomite_se.utils module

dolomite_se.utils.read_common_se_props(path, **kwargs)[source]

Read shared properties from a directory containing SummarizedExperiment or its derivatives.

Parameters:

path – Path to the directory containing the object.

Returns:

A tuple containing row data, column data and the assays.

dolomite_se.utils.save_common_se_props(x, path, data_frame_args, assay_args, **kwargs)[source]

Save common SummarizedExperiment properties to the specified path.

Mostly for reuse in derivatives of SE.

Parameters:

  • x – Object to be staged.

  • path – Path to a directory in which to save x.

  • data_frame_args – Further arguments to pass to the save_object method for the row/column data.

  • assay_args – Further arguments to pass to the save_object method for the assays.

Module contents