• Read5 is a python wrapper to read fast5, slow5/blow5 and pod5 files using the same overloaded functions from different APIs.
• Read5_ont is a python wrapper to read fast5 and pod5 files using the same overloaded functions from different APIs.

Table of Content

1. Installation
2. Usage
3. Full Documentation ___ ## Installation

Pypi/pip

bash pip install read5_ont

Conda

Pod5 is now available via conda (19.07.2023).

bash conda create -n read5_ont -c jannessp read5_ont conda activate read5_ont

Usage

Click here to see a full documentation about the classes and function.

my_file can be a fast5 or pod5 file. The wrapper detects the file format depending on the file extension.

You might encounter errors with python 3.13. AFAIK there is some dependency problem with pyarrow and other libraries for python 3.13, but I could not fix it..

Small example:

```python from read5 import read # or from read5.Reader import read

r5 = read(myfile) # file with one of these extensions: .fast5, .pod5 for readid in r5: signal = r5.getSignal(readid) # returns raw integer values stored in the file pAsignal = r5.getpASignal(readid) # returns pA signal normsignal = r5.getZNormSignal(readid) # returns normalised read signal: normsignal = (signal - median(signal)) / mad(signal) polyAstdSignal = r5.getPolyAStandardizedSignal(readid, polyAstart, polyAend) # returns polyA standardized read signal # default polyAMean : float = 108.901413, polyAStdev : float = 2.676522, this can be changed using the parameters channel = r5.getChannelNumber(readid) sampleid = r5.getSampleID(readid) runid = r5.getRunID(readid)

readid_list = r5.getReads() ```

File Reader Classes

If you want to use the file readers you can import the corresponding class like this:

python from read5.Fast5Reader import Fast5Reader # contains the Fast5 Reader class from read5.Slow5Reader import Slow5Reader # contains the Slow5 Reader class - !not available in read5_ont! from read5.Pod5Reader import Pod5Reader # contains the Pod5 Reader class

Abstract File Reader Class

python from read5.AbstractFileReader import AbstractFileReader

Possible Exceptions

python from read5.Exceptions import UnknownFileFormatException, UnknownNormalizationMode

• UnknownFileFormatException: is raised, when the file extension does not match one of '.fast5', '.slow5', '.blow5', '.pod5'
• UnknownNormalizationMode: is raised, when an unknown mode is provided for the signal normalization function

Full Documentation

Created with pdoc3. Can be found here.