script to generate amplicon coverage plot
Project description
amplicon_coverage_plot
The script will generate an interactive barplot given amplicon info in bed/bedpe format and coverage information in cov/bam file.
Dependencies
Programming/Scripting languages
- Python >=v3.7
- The pipeline has been tested in v3.7.6
Python packages
Third party softwares/packages
- samtools >=1.9 - process bam file
Installation
Install by pip
pip install amplicov
Install from source
Clone the amplicon_coverage_plot
repository.
git clone https://github.com/chienchi/amplicon_coverage_plot
Then change directory to amplicon_coverage_plot
and install.
cd amplicon_coverage_plot
python setup.py install
If the installation was succesful, you should be able to type amplicon_coverage.py -h
and get a help message on how to use the tool.
amplicov -h
Usage
usage: amplicov [-h] (--bed [FILE] | --bedpe [FILE])
(--bam [FILE] | --cov [FILE]) [-o [PATH]] [-p [STR]] [--pp]
[--version]
Script to parse amplicon region coverage and generate barplot in html
optional arguments:
-h, --help show this help message and exit
--pp process proper paired only reads from bam file
(illumina)
--version show program's version number and exit
Amplicon Input (required, mutually exclusive):
--bed [FILE] amplicon bed file
--bedpe [FILE] amplicon bedpe file
Coverage Input (required, mutually exclusive):
--bam [FILE] sorted bam file (ex: samtools sort input.bam -o sorted.bam)
--cov [FILE] coverage file [position coverage]
Output:
-o [PATH], --outdir [PATH]
output directory
-p [STR], --prefix [STR]
output prefix
Test
cd tests
./runTest.sh
Outputs
-- prefix_amplicon_coverage.txt
ID | Whole_Amplicon | Unique |
---|---|---|
nCoV-2019_1 | 217.74 | 53.18 |
nCoV-2019_2 | 1552.83 | 1235.50 |
nCoV-2019_3 | 3164.22 | 2831.73 |
nCoV-2019_4 | 2005.16 | 1658.00 |
etc... |
Table Header Definition in the amplicon_coverage.txt
-- prefix_amplicon_coverage.html
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