Skip to main content

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

Project description

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

Alternatively you can create the environment using the conda.recipe/env.yml file.

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.

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
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’]

  • UnknownNormalizationMode: is raised, when an unknown mode is provided for the signal normalization function

Full Documentation

Created with pdoc3. Can be found here.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

read5-1.2.4.tar.gz (1.5 MB view details)

Uploaded Source

Built Distribution

read5-1.2.4-py2.py3-none-any.whl (26.9 kB view details)

Uploaded Python 2 Python 3

File details

Details for the file read5-1.2.4.tar.gz.

File metadata

  • Download URL: read5-1.2.4.tar.gz
  • Upload date:
  • Size: 1.5 MB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/4.0.2 CPython/3.11.6

File hashes

Hashes for read5-1.2.4.tar.gz
Algorithm Hash digest
SHA256 447f22c62c74e8579744fb9a0fc30109f4ee2031b6fd86072608ee4f5dfd5c5b
MD5 0cc2e55bcc5e0aa38aae19fe170d2bc4
BLAKE2b-256 d5e18e11165500c6e026d28daca771942a7c8f8c1daf8e4dd243ce633cc491ff

See more details on using hashes here.

File details

Details for the file read5-1.2.4-py2.py3-none-any.whl.

File metadata

  • Download URL: read5-1.2.4-py2.py3-none-any.whl
  • Upload date:
  • Size: 26.9 kB
  • Tags: Python 2, Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/4.0.2 CPython/3.11.6

File hashes

Hashes for read5-1.2.4-py2.py3-none-any.whl
Algorithm Hash digest
SHA256 9f953899514cba5719e2eb20c5d86a495bedc37210d9c4fd892e86cf505726fe
MD5 153f400aae408c373c08c67642614273
BLAKE2b-256 457202cae0e36689cd2e3d2eba1c39b857a04d0dbb4107015939e071e5114d01

See more details on using hashes here.

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page