https://github.com/rnajena/read5_ont
Wrapper to read fast5 and pod5 files.
https://github.com/rnajena/read5_ont
fast5 ont oxford-nanopore oxford-nanopore-data pod5 raw-data
Last synced: 20 days ago
JSON representation
Wrapper to read fast5 and pod5 files.
- Host: GitHub
- URL: https://github.com/rnajena/read5_ont
- Owner: rnajena
- License: gpl-3.0
- Created: 2023-11-24T17:48:25.000Z (about 2 years ago)
- Default Branch: main
- Last Pushed: 2025-04-05T20:27:25.000Z (10 months ago)
- Last Synced: 2025-09-29T10:28:21.102Z (4 months ago)
- Topics: fast5, ont, oxford-nanopore, oxford-nanopore-data, pod5, raw-data
- Language: Python
- Homepage: https://jannessp.github.io/read5.github.io/
- Size: 814 KB
- Stars: 2
- Watchers: 1
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Citation: CITATION.cff
Awesome Lists containing this project
README
# 
- [**Read5**](https://github.com/JannesSP/read5) is a python wrapper to read fast5, slow5/blow5 and pod5 files using the same overloaded functions from different APIs. 
- [**Read5_ont**](https://github.com/JannesSP/read5_ont) is a python wrapper to read fast5 and pod5 files using the same overloaded functions from different APIs. 
[](https://www.gnu.org/licenses/gpl-3.0)
[  ](https://pypi.org/project/read5_ont/)
[](https://anaconda.org/jannessp/read5_ont)  [](https://anaconda.org/jannessp/read5_ont) [](https://anaconda.org/jannessp/read5_ont)
[](https://zenodo.org/badge/latestdoi/633012569)
[](https://twitter.com/Ja_Spangenberg)
___
## Table of Content
1. [Installation](#installation)
2. [Usage](#usage)
3. [Full Documentation](https://jannessp.github.io/read5.github.io/)
___
## Installation
### Pypi/pip
```bash
pip install read5_ont
```
### Conda
Pod5 is now available via [conda](https://anaconda.org/jannessp/pod5) (19.07.2023).
```bash
conda create -n read5_ont -c jannessp read5_ont
conda activate read5_ont
```
___
## 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 or pod5 file. The wrapper detects the file format depending on the file extension.
You might encounter errors with python 3.13. AFAIK there is some dependency problem with pyarrow and other libraries for python 3.13, but I could not fix it..
### Small example:
```python
from read5 import read # or from read5.Reader import read
r5 = read(my_file) # file with one of these extensions: .fast5, .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
# default polyAMean : float = 108.901413, polyAStdev : float = 2.676522, this can be changed using the parameters
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:
```python
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
```python
from read5.AbstractFileReader import AbstractFileReader
```
### Possible Exceptions
```python
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
## Full Documentation
Created with [pdoc3](https://pdoc3.github.io/pdoc/).
Can be found [here](https://jannessp.github.io/read5.github.io/).