Installation
------------
Pypi/pip
~~~~~~~~
.. code:: bash
pip install read5
Conda
~~~~~
Pod5 is now available via `conda <https://anaconda.org/jannessp/pod5>`__ (19.07.2023).
.. code:: bash
conda install mamba
mamba create -n read5 -c jannessp read5
conda activate read5
Alternatively you can create the environment using the
`conda.recipe/env.yml <conda.recipe/env.yml>`__ file.
.. code:: bash
conda install mamba
mamba env create -f conda.recipe/env.yml
conda activate read5
--------------
Usage
-----
`Click here to see a full documentation about the classes and
function. <https://jannessp.github.io/read5.github.io/>`__
*my_file* can be a fast5, slow5, blow5 or pod5 file. The wrapper detects
the file format depending on the file extension.
Small example:
~~~~~~~~~~~~~~
.. code:: python
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:
.. code:: python
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
Abstract File Reader Class
~~~~~~~~~~~~~~~~~~~~~~~~~~
.. code:: python
from read5.AbstractFileReader import AbstractFileReader
Possible Exceptions
~~~~~~~~~~~~~~~~~~~
.. code:: 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 <https://pdoc3.github.io/pdoc/>`__. Can be found
`here <https://jannessp.github.io/read5.github.io/>`__.
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