# amplicon_coverage_plot
[](https://doi.org/10.5281/zenodo.7531741)
[](https://anaconda.org/bioconda/amplicon_coverage_plot)
[](https://travis-ci.org/chienchi/amplicon_coverage_plot)
[](https://codecov.io/gh/chienchi/amplicon_coverage_plot)
[](https://badge.fury.io/py/amplicov)
The script will generate an [interactive barplot](https://chienchi.github.io/amplicon_coverage_plot/index.html) given amplicon info in [bed6/bedpe](https://bedtools.readthedocs.io/en/latest/content/general-usage.html) format and coverage information in cov/bam file.
## Dependencies
### Programming/Scripting languages
- [Python >=v3.8](https://www.python.org/)
- The pipeline has been tested in v3.8.10
### Python packages
- [numpy >=1.15.1](http://www.numpy.org/)
- [plotly >=4.7.1](https://plotly.com/python/)
- [pysam >= 0.15.4](https://github.com/pysam-developers/pysam)
### Third party softwares/packages
- [samtools >=1.9](http://www.htslib.org) - process bam file
## Installation
### Install by pip
```
pip install amplicov
```
### Install by conda
```
conda install -c bioconda amplicon_coverage_plot
```
### 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 `amplicov -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]
[--mincov [INT]] [--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)
--count_primer count overlapped primer region to unqiue coverage
--mincov [INT] minimum coverage to count as ambiguous N site
[default:10]
-r [STR], --refID [STR]
reference accession (bed file first field)
--depth_lines DEPTH_LINES [DEPTH_LINES ...]
Add option to display lines at these depths (provide depths as a list of integers) [default:5 10 20 50]
--gff [FILE] gff file for data hover info annotation
--version show program's version number and exit
Amplicon Input (required, mutually exclusive):
--bed [FILE] amplicon bed file (bed6 format)
--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 | Whole_Amplicon_Ns(cov<10) | Unique_Amplicon_Ns(cov<10) |
|-------------|----------------|---------|---------------------------|----------------------------|
| nCoV-2019_1 | 217.74 | 53.00 | 0.00 | 0.00 |
| nCoV-2019_2 | 1552.83 | 1235.50 | 0.00 | 0.00 |
| nCoV-2019_3 | 3164.22 | 2831.73 | 0.00 | 0.00 |
| nCoV-2019_4 | 2005.16 | 1658.00 | 0.00 | 0.00 |
| etc... | | | | |
#### Table Header Definition in the amplicon_coverage.txt
<img width="465" alt="Screen Shot 2020-06-15 at 3 29 53 PM" src="https://user-images.githubusercontent.com/737589/84708117-1fc2e480-af1d-11ea-8411-35210a8dd6fa.png">
* Whole_Amplicon_Ns(cov<10): The number of aligned position with coverage < 10 or (--mincov) in the Whole Amplicon region
* Unique_Amplicon_Ns(cov<10): The number of aligned position with coverage < 10 or (--mincov) in the Unique region
-- prefix_amplicon_coverage.html
```color black for < 5x and blue for <20x```
<a href="https://chienchi.github.io/amplicon_coverage_plot/index.html"></a>
Raw data
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"description": "# amplicon_coverage_plot\n[](https://doi.org/10.5281/zenodo.7531741)\n[](https://anaconda.org/bioconda/amplicon_coverage_plot)\n[](https://travis-ci.org/chienchi/amplicon_coverage_plot)\n[](https://codecov.io/gh/chienchi/amplicon_coverage_plot)\n[](https://badge.fury.io/py/amplicov)\n\nThe script will generate an [interactive barplot](https://chienchi.github.io/amplicon_coverage_plot/index.html) given amplicon info in [bed6/bedpe](https://bedtools.readthedocs.io/en/latest/content/general-usage.html) format and coverage information in cov/bam file.\n\n## Dependencies\n\n### Programming/Scripting languages\n- [Python >=v3.8](https://www.python.org/)\n - The pipeline has been tested in v3.8.10\n\n### Python packages\n- [numpy >=1.15.1](http://www.numpy.org/) \n- [plotly >=4.7.1](https://plotly.com/python/)\n- [pysam >= 0.15.4](https://github.com/pysam-developers/pysam)\n\n### Third party softwares/packages\n- [samtools >=1.9](http://www.htslib.org) - process bam file\n\n## Installation\n\n### Install by pip\n\n```\npip install amplicov\n```\n\n### Install by conda\n\n```\nconda install -c bioconda amplicon_coverage_plot \n```\n\n### Install from source\nClone the `amplicon_coverage_plot` repository.\n\n```\ngit clone https://github.com/chienchi/amplicon_coverage_plot\n```\n\nThen change directory to `amplicon_coverage_plot` and install.\n\n```\ncd amplicon_coverage_plot\npython setup.py install\n```\n\nIf the installation was succesful, you should be able to type `amplicov -h` and get a help message on how to use the tool.\n\n```\namplicov -h\n```\n\n\n## Usage\n```\nusage: amplicov [-h] (--bed [FILE] | --bedpe [FILE])\n (--bam [FILE] | --cov [FILE]) [-o [PATH]] [-p [STR]] [--pp]\n [--mincov [INT]] [--version]\n\nScript to parse amplicon region coverage and generate barplot in html\n\noptional arguments:\n -h, --help show this help message and exit\n --pp process proper paired only reads from bam file\n (illumina)\n --count_primer count overlapped primer region to unqiue coverage\n --mincov [INT] minimum coverage to count as ambiguous N site\n [default:10]\n -r [STR], --refID [STR]\n reference accession (bed file first field)\n --depth_lines DEPTH_LINES [DEPTH_LINES ...]\n Add option to display lines at these depths (provide depths as a list of integers) [default:5 10 20 50]\n --gff [FILE] gff file for data hover info annotation\n --version show program's version number and exit\n\nAmplicon Input (required, mutually exclusive):\n --bed [FILE] amplicon bed file (bed6 format)\n --bedpe [FILE] amplicon bedpe file\n\nCoverage Input (required, mutually exclusive):\n --bam [FILE] sorted bam file (ex: samtools sort input.bam -o\n sorted.bam)\n --cov [FILE] coverage file [position coverage]\n\nOutput:\n -o [PATH], --outdir [PATH]\n output directory\n -p [STR], --prefix [STR]\n output prefix\n```\n\n## Test\n\n```\ncd tests\n./runTest.sh\n```\n\n## Outputs \n\n-- prefix_amplicon_coverage.txt\n\n| ID | Whole_Amplicon | Unique | Whole_Amplicon_Ns(cov<10) | Unique_Amplicon_Ns(cov<10) |\n|-------------|----------------|---------|---------------------------|----------------------------|\n| nCoV-2019_1 | 217.74 | 53.00 | 0.00 | 0.00 |\n| nCoV-2019_2 | 1552.83 | 1235.50 | 0.00 | 0.00 |\n| nCoV-2019_3 | 3164.22 | 2831.73 | 0.00 | 0.00 |\n| nCoV-2019_4 | 2005.16 | 1658.00 | 0.00 | 0.00 |\n| etc... | | | | |\n\n#### Table Header Definition in the amplicon_coverage.txt \n\n<img width=\"465\" alt=\"Screen Shot 2020-06-15 at 3 29 53 PM\" src=\"https://user-images.githubusercontent.com/737589/84708117-1fc2e480-af1d-11ea-8411-35210a8dd6fa.png\">\n\n* Whole_Amplicon_Ns(cov<10): The number of aligned position with coverage < 10 or (--mincov) in the Whole Amplicon region\n\n* Unique_Amplicon_Ns(cov<10): The number of aligned position with coverage < 10 or (--mincov) in the Unique region\n\n-- prefix_amplicon_coverage.html\n\n```color black for < 5x and blue for <20x```\n\n<a href=\"https://chienchi.github.io/amplicon_coverage_plot/index.html\"></a>\n\n",
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