Python API Reference¶

This is the reference for the classes and functions in the poreFlow module.

Most used classes¶

Class	Description
poreflow.File	input/output to `.fast5` and `.dat` files.
poreflow.RawDataFrame	Table for storing full measurements on a single channel
poreflow.EventsDataFrame	Table for storing events and their properties
poreflow.EventDataFrame	Table for storing an event and its current data
poreflow.StepsDataFrame	Table for storing steps for one or more events

Submodules and classes related to events.

Class	Description
poreflow.EventsDataFrame	Table for storing events and their properties
poreflow.EventDataFrame	Table for storing an event and its current data
poreflow.events.detection	Submodule for detecting events in measurements
poreflow.events.open_state	Submodule for detecting an open state in a measurement
poreflow.events.voltage_state	Submodule for detecting whether the voltage is in range during a measurement
poreflow.steps.metrics	Metrics used to describe an event based on step information
poreflow.events.selection	Submodule for describing events using features and selecting good events by these features

Submodules and classes related to steps.

Class	Description
poreflow.StepsDataFrame	Table for storing steps for a single or many events
poreflow.steps.changepoint	Information-theory based change point detection algorithm written in C++
poreflow.steps.cpic	Change Point Information Criterion calculation functions
poreflow.steps.metrics	Metrics used to describe an event based on step information
poreflow.steps.predict	Submodule to predict a step sequence from a DNA nucleotide sequence
poreflow.steps.sequence	(Work in progress) Hidden Markov Model's for sequencing/variant calling

General tools

Class	Description
poreflow.constants	Constants used throughout poreFlow
poreflow.utils	General utility functions

Plotting tools

Class	Description
poreflow.plots	Plotting helper functions

Plotting tools

Class	Description
poreflow.parallel	Tools for monitoring multiprocessing tasks