Python package for upstream preprocessing and downstream analysis of nanopolish
- Author: Adrien Leger - aleg {at} ebi.ac.uk
- URL: https://github.com/a-slide/NanopolishComp
- Licence: MIT
- Python version: >=3.3
Ideally, before installation, create a clean python3 virtual environment to deploy the package, using virtualenvwrapper for example (see http://www.simononsoftware.com/virtualenv-tutorial-part-2/).
Nanopolish 0.10+ is required to generate the files used by several commands from this package
All python dependencies are automatically installed with pip
Ideally, before installation, create a clean python3 virtual environment to deploy the package, using virtualenvwrapper for example (see http://www.simononsoftware.com/virtualenv-tutorial-part-2/).
-
To install the package
pip3 install git+https://github.com/a-slide/NanopolishComp.git -
To update the package:
pip3 install git+https://github.com/a-slide/NanopolishComp.git --upgrade
- Eventalign_collapse This program collapses the raw file generated by nanopolish eventalign by kmers rather than by event.
The following fields are discarded: strand, event_index, model_kmer, model_mean, model_stdv, standardized_level, samples
If using the --signal-index option the start_idx and end_idx are updated to correspond to the entire kmer signal.
If using the --samples mean, median, std and variance are computed for each kmer based on the raw datapoint
The package has a command line interface and a Python API.
The usage is detailed in the usage jupyter notebook
Please be aware that NanopolishComp is an experimental package that is still under development. It was tested under Linux Ubuntu 16.04 and in an HPC environment running under Red Hat Enterprise 7.1.
You are welcome to contribute by requesting additional functionalities, reporting bugs or by forking and submitting patches or updates pull requests
Thank you