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

Project description

Installation

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

pip install 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)
    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.

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