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|
nanomath
========
This module provides a few simple math and statistics functions for
other scripts processing Oxford Nanopore sequencing data
|Twitter URL| |install with conda| |install with Debian|
FUNCTIONS
---------
- Calculate read N50 from a set of lengths ``get_N50(readlenghts)``
- Remove extreme length outliers from a dataset
``remove_length_outliers(dataframe, columname)``
- Calculate the average Phred quality of a read
``ave_qual(qualscores)``
- Write out the statistics report after calling readstats function
``write_stats(dataframe, outputname)``
- Compute a number of statistics, return a dictionary
``calc_read_stats(dataframe)``
As of **v1.3.0**, nanomath calculates the average quality differently,
by first converting per-read phred scale averages to error rates, take
the average, and converting back
(`nanostat#40 <https://github.com/wdecoster/nanostat/issues/40>`__)
INSTALLATION
------------
.. code:: bash
pip install nanomath
| or
| |install with conda|
::
conda install -c bioconda nanomath
CONTRIBUTORS
------------
[@alexomics](https://github.com/alexomics) for fixing the indentation of
the printed stats
CITATION
--------
If you use this tool, please consider citing our
`publication <https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty149/4934939>`__.
.. |Twitter URL| image:: https://img.shields.io/twitter/url/https/twitter.com/wouter_decoster.svg?style=social&label=Follow%20%40wouter_decoster
:target: https://twitter.com/wouter_decoster
.. |install with conda| image:: https://anaconda.org/bioconda/nanomath/badges/installer/conda.svg
:target: https://anaconda.org/bioconda/nanomath
.. |install with Debian| image:: https://www.debian.org/logos/button-mini.png
:target: https://tracker.debian.org/pkg/python-nanomath
|
