zhoulytwinyu/coverage-py

coverage

This module calculate the read coverage for each loci, given nucleotide reads and loci of interest,

Install

pip install git+https://www.github.com/zhoulytwinyu/coverage-py

Usage

Python interface

You can import functions to calculate coveraged:

from coverage import get_coverages_bisect
get_coverages_bisect

Command line interface

A command line script is included in the package. Once the package is installed using pip, you can call:

get_coverages.py <READS_CSV> <LOCI_CSV> <OUTPUT_CSV>

where

• READS_CSV is a csv containing "start" and "length"
• LOCI_CSV is a csv containing "position"
• OUTPUT_CSV is the output, a csv containing "position" and "coverage"

Unittest

You can verify the module works correctly by running unittest we provided. In command line:

git clone https://www.github.com/zhoulytwinyu/coverage-py.git
cd coverage-py
python3 setup.py test

The unittest randomly generate reads and loci, in silico and then crosscheck the results from two methods: get_coverages_bisect and get_coverages_loop. The idea is that random, simulated test may cover more corner cases and the two methods provide the same result only when both of them works correctly.