Science Score: 54.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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✓Academic publication links
Links to: zenodo.org -
○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (11.4%) to scientific vocabulary
Keywords
Repository
Wrapper to read fast5, slow5, blow5 and pod5 files.
Basic Info
- Host: GitHub
- Owner: rnajena
- License: gpl-3.0
- Language: Python
- Default Branch: main
- Homepage: https://jannessp.github.io/read5.github.io/
- Size: 1.67 MB
Statistics
- Stars: 13
- Watchers: 1
- Forks: 1
- Open Issues: 1
- Releases: 20
Topics
Metadata Files
README.md
- Read5 is a python wrapper to read fast5, slow5/blow5 and pod5 files using the same overloaded functions from different APIs.
- Read5_ont is a python wrapper to read fast5 and pod5 files using the same overloaded functions from different APIs.
Table of Content
- Installation
- Usage
- Full Documentation ___ ## Installation
Pypi/pip
bash
pip install read5
Conda
Pod5 is now available via conda (19.07.2023).
bash
conda create -n read5 -c jannessp read5
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:
```python from read5 import read # or from read5.Reader import read
r5 = read(myfile) # file with one of these extensions: .fast5, .slow5, .blow5, .pod5 for readid in r5: signal = r5.getSignal(readid) # returns raw integer values stored in the file pAsignal = r5.getpASignal(readid) # returns pA signal normsignal = r5.getZNormSignal(readid) # returns normalized read signal: normsignal = (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'
- UnknownNormalizationMode: is raised, when an unknown mode is provided for the signal normalization function
Full Documentation
Owner
- Name: RNA Bioinformatics and Highthroughput Analysis Jena
- Login: rnajena
- Kind: user
- Location: Jena
- Website: rna.uni-jena.de
- Repositories: 2
- Profile: https://github.com/rnajena
Citation (CITATION.cff)
cff-version: 1.2.1
message: "If you use this software, please cite it as below."
authors:
- family-names: "Spangenberg"
given-names: "Jannes"
orcid: "https://orcid.org/0000-0002-6126-411X"
title: "Read5"
version: 1.2.6
date-released: 2023-07-11
identifiers:
- type: doi
value: 10.5281/zenodo.10785021
GitHub Events
Total
- Release event: 2
- Watch event: 3
- Push event: 7
- Create event: 1
Last Year
- Release event: 2
- Watch event: 3
- Push event: 7
- Create event: 1
Packages
- Total packages: 1
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Total downloads:
- pypi 52 last-month
- Total dependent packages: 1
- Total dependent repositories: 0
- Total versions: 12
- Total maintainers: 1
pypi.org: read5
Wrapper to read fast5 and pod5 files.
- Documentation: https://read5.readthedocs.io/
- License: GNUv3
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Latest release: 1.2.8
published 11 months ago