rnalysis.filtering.Pipeline

class rnalysis.filtering.Pipeline(filter_type: ~typing.Union[str, ~rnalysis.filtering.Filter, ~rnalysis.filtering.CountFilter, ~rnalysis.filtering.DESeqFilter, ~rnalysis.filtering.FoldChangeFilter] = <class 'rnalysis.filtering.Filter'>)

A collection of functions to be applied sequentially to Filter objects.

Attributes

functions: list

A list of the functions in the Pipeline.

params: list

A list of the parameters of the functions in the Pipeline.

filter_type: Filter object

The type of Filter objects to which the Pipeline can be applied

__init__(filter_type: ~typing.Union[str, ~rnalysis.filtering.Filter, ~rnalysis.filtering.CountFilter, ~rnalysis.filtering.DESeqFilter, ~rnalysis.filtering.FoldChangeFilter] = <class 'rnalysis.filtering.Filter'>)

Parameters

filter_type (str or Filter object (default=filtering.Filter)) – the type of Filter object the Pipeline can be applied to.

Examples

>>> from rnalysis import filtering
>>> pipe = filtering.Pipeline()
>>> deseq_pipe = filtering.Pipeline('deseqfilter')

Pipeline.add_function(func, *args, **kwargs)	Add a function to the pipeline.
Pipeline.apply_to(filter_object[, inplace])	Sequentially apply all functions in the Pipeline to a given Filter object.
Pipeline.export_pipeline(filename)	Export a Pipeline to a Pipeline YAML file or YAML-like string.
Pipeline.import_pipeline(filename)	Import a Pipeline from a Pipeline YAML file or YAML-like string.
Pipeline.remove_last_function()	Removes from the Pipeline the last function that was added to it.