Pyth-ion is a python based program designed for analysis of nanopore ionic current data.
The software provides a viewer for a variety of file types including .log (Chimera Amplifiers), .abf (Axopatch), .opt (General Binary), or .csv (standard text files). Assumptions are made in regards to the structure of each of these as the program requires information on sampling rate and low-pass filter value, so some type of supplementary file containing settings is usually assumed (the .log file usually has an accompanying .mat for example, for .abf these are contained in the header).
If any assistance is required in tailoring the software to your file type, please email roberthenley89@gmail.com, or report an issue here on Github
Two methods are provided for analyzing translocation data, the first being the standard event detection analysis. The software does a primitive baseline detection but for accurate analysis a user set baseline is required. For more information see the user guide. After this simple event detection, a database file is generated in the same folder as the analyzed file. This file has the same name as the analyzed file, followed by DB.txt (i.e. mydata.log generates a file named mydataDB.txt). This file is a tab seperated file that contains 4 columns. The columns have the following order: Current Blockade,Fractional Current Blockade, Dwell Time, Inter-Event Time, and Standard-deviation of current values.
The simple analysis also generates a .pkl file, this file contains the start and end points of the events detected in the simple analysis. In many cases the simple analysis does not give the correct current blockade. This is because the algorithm simply takes the mean blockade value over the course of the event, if the event has multiple levels and the user desires the blockade depth of the deepest level they can take advantage of the Batch Process analysis. This analysis implements a self-correcting CUSUM algorithm to find all of the event levels and produces a new analysis file (i.e. mydata.pkl generates a file named mydatallDB.txt) where the blockade depth that is reported is the deepest stable level that is detected.
This package can be easily run from a standard Anaconda 3 distribution, the only additional requirement being pyqtgraph