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Recent Releases of read5

read5 - 1.2.8

Added

  • __setstate__ and __getstate__ functions to make the reader objects pickable

Changed

  • to new building system using pyproject.toml instead of setyp.py

- Python
Published by JannesSP about 1 year ago

read5 - 1.2.5

  • update to python 3.12

- Python
Published by JannesSP over 1 year ago

read5 - 1.2.4

Changed

Extend getPolyAStandardizedSignal - add mode change between median and mean - standardization parameters can be added as parameters

- Python
Published by JannesSP about 2 years ago

read5 - 1.2.3

Added

  • getPolyAStandardizedSignal(self, readid : str, polyAstart : int, polyAend : int) -> np.ndarray

Standardize the read signal of the provided read with the polyA. This function uses the median and mad to standardize the read with the polyA signal. After standardization the polyA signal will have a mean of 108.901413 and a stdev of 2.676522.

Parameter

readid : str polyAstart : int - included starting index of the polyA signal in the read

polyAend : int - excluded ending index of the polyA signal in the read

Returns

standardizedSignal : np.ndarray - polyA standardized read signal

- Python
Published by JannesSP about 2 years ago

read5 - 1.2.1

Changed

Update Versioneer README fixes here and there

Added

- Python
Published by JannesSP over 2 years ago

read5 - 1.2.0

Changed Conda Recipe

- Python
Published by JannesSP almost 3 years ago

read5 - 1.1.9

Move python requirements in setup.py to 'pythonrequires' instead of 'installrequires'

- Python
Published by JannesSP almost 3 years ago

read5 - 1.1.8

Add test files to sdist by adding "graft tests" to MANIFEST.in

- Python
Published by JannesSP almost 3 years ago

read5 - 1.1.7

Added - getFilePath() method to access the _filepath variable - activate tests for conda package build

- Python
Published by JannesSP almost 3 years ago

read5 - 1.1.6

Fixed Imports of Conda Package

- Python
Published by JannesSP almost 3 years ago

read5 - 1.1.5

Update README.rst for pipy

- Python
Published by JannesSP almost 3 years ago

read5 - 1.1.4

Add README.rst for pipy

- Python
Published by JannesSP almost 3 years ago

read5 - 1.1.3

Remove long description

- Python
Published by JannesSP almost 3 years ago

read5 - 1.1.2

Changes - Fixed Import Commands (hopefully) - update docs - update README - change long description type in setup.py

- Python
Published by JannesSP almost 3 years ago

read5 - 1.1.1

Package is buildable and runable via pip. Conda does still not work.

- Python
Published by JannesSP almost 3 years ago

read5 - 1.1.0

Basically the same as 1.0.0 (https://github.com/JannesSP/read5/releases/tag/1.0.0, commit: 4020097) - but changed to version number 1.1.0 to avoid confusion!

Changes - read5 should be importable now - fixed init.py and conda recipe - Add 'Abstract' to abstract class and file 'FileReader' - Change 'read.py' to 'Reader.py' - Rename 'open' function to 'read5'

Added - Added basic functions to read data from fast5, slow5/blow5 and pod5 - Added tests to test all basic functions - Launched documentation site under https://jannessp.github.io/read5.github.io/ - Add exception tests

Conda - update recipe - switch to find_packages() in setup.py

Others - Update READMEs

- Python
Published by JannesSP almost 3 years ago

read5 - 1.0.0

Switched back to version 1.0.0 as read5 was not importable before using Conda.

Changes - read5 should be importable now - fixed init.py and conda recipe - Add 'Abstract' to abstract class and file 'FileReader' - Change 'read.py' to 'Reader.py' - Rename 'open' function to 'read5'

Added - Added basic functions to read data from fast5, slow5/blow5 and pod5 - Added tests to test all basic functions - Launched documentation site under https://jannessp.github.io/read5.github.io/ - Add exception tests

Conda - update recipe - switch to find_packages() in setup.py

Others - Update READMEs

- Python
Published by JannesSP almost 3 years ago

read5 - 0.1.2

  • Update Conda Dependencies
  • Prepare Conda Package Without POD5
    • Install POD5 via pip in the environment!

- Python
Published by JannesSP about 3 years ago

read5 - 0.1.1

First Prototype of Read5

  • Reading fast5, slow5, blow5 and pod5 using overloaded functions.
  • Testing files & tests

  • Conda recipe

  • Reading read:

    • signal, pA signal and normalized signal
    • calibration & normalization parameter
    • start time
    • channel number
    • sampling rate

  • Running tests after conda build automatically

- Python
Published by JannesSP about 3 years ago

read5 - 0.1.0

First Prototype of Read5

  • Reading fast5, slow5, blow5 and pod5 using overloaded functions.
  • Testing files & tests

  • Conda recipe

  • Reading read:

    • signal, pA signal and normalized signal
    • calibration & normalization parameter
    • start time
    • channel number
    • sampling rate

- Python
Published by JannesSP about 3 years ago