wip/nanomath 1.2.1.20210604 NetBSD
Math functions for other Oxford Nanopore processing scripts
- System
- NetBSD
- Repository
- pkgsrc-wip
- Maintainer
- [email protected]
- License
- gnu-gpl-v3
- Categories
- wip, biology, python
Description
This module provides a few simple math and statistics functions for other scripts processing Oxford Nanopore sequencing data
## 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)`
If you use this tool, please consider citing our publication: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty149/4934939.
Install
From pkgsrc-wip (no binary package):
cd /usr/pkgsrc/wip/nanomath && make install clean