The read5 from rnajena

read5's Introduction

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

Installation

Pypi/pip

pip install read5

Conda

Pod5 is now available via conda (19.07.2023).

conda install mamba
mamba create -n read5 -c jannessp read5
conda activate read5

Usage

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

my_file can be a fast5, slow5, blow5 or pod5 file. The wrapper detects the file format depending on the file extension.

Small example:

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

r5 = read(my_file) # file with on of these extensions: .fast5, .slow5, .blow5, .pod5
for readid in r5:
    signal = r5.getSignal(readid) # returns raw integer values stored in the file
    pA_signal = r5.getpASignal(readid) # returns pA signal
    norm_signal = r5.getZNormSignal(readid) # returns normalised read signal: norm_signal = (signal - median(signal)) / mad(signal)
    polyAstdSignal = r5.getPolyAStandardizedSignal(readid, polyAstart, polyAend) # returns polyA standardized read signal
    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:

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

from read5.AbstractFileReader import AbstractFileReader

Possible Exceptions

from read5.Exceptions import UnknownFileFormatException, UnknownNormalizationMode

UnknownFileFormatException: is raised, when the file extension does not match one of ['.fast5', '.slow5', '.blow5', '.pod5'] (or ['.fast5', '.pod5'] in read5_ont)
UnknownNormalizationMode: is raised, when an unknown mode is provided for the signal normalization function