read5 1.1.6

Wrapper to read fast5, slow5, blow5 and pod5 files.

Installation

Pod5 is not available via conda (27.06.2023). Read5 Currently available via pipy.

pip install read5

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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)
    norm_signal = r5.getZNormSignal(readid) # returns normalised read signal: norm_signal = (signal - median(signal)) / mad(signal)
    channel = r5.getChannelNumber(readid)
    sampleid = r5.getSampleID(readid)
    runid = r5.getSampleID(readid)

readid_list = r5.getReads()

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
from read5.Pod5Reader import Pod5Reader # contains the Pod5 Reader class

Full Documentation

Created with pdoc3. Can be found here.