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https://github.com/cmdoret/tinycov
Command line tool to plot genomic coverage from a BAM file
https://github.com/cmdoret/tinycov
coverage genomics-visualization rolling-windows
Last synced: about 2 months ago
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Command line tool to plot genomic coverage from a BAM file
- Host: GitHub
- URL: https://github.com/cmdoret/tinycov
- Owner: cmdoret
- License: other
- Created: 2019-11-05T13:54:11.000Z (about 5 years ago)
- Default Branch: master
- Last Pushed: 2023-04-05T10:13:51.000Z (over 1 year ago)
- Last Synced: 2024-08-09T14:59:11.418Z (5 months ago)
- Topics: coverage, genomics-visualization, rolling-windows
- Language: Python
- Homepage:
- Size: 34.8 MB
- Stars: 13
- Watchers: 2
- Forks: 4
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
### tinycov
[](https://badge.fury.io/py/tinycov) [](https://github.com/cmdoret/tinycov/actions/workflows/python-tests.yml) [](https://codecov.io/gh/cmdoret/tinycov) [](https://www.codacy.com/gh/cmdoret/tinycov/dashboard?utm_source=github.com&utm_medium=referral&utm_content=cmdoret/tinycov&utm_campaign=Badge_Grade) [](https://github.com/psf/black)
Tinycov is a small standalone command line utility written in python to plot the coverage of a BAM file quickly.
This software was inspired by [Matt Edwards' genome coverage plotter](https://github.com/matted/genome_coverage_plotter).
### Installation
To install the stable version:
```pip3 install --user tinycov```
To install the development version:
```
git clone https://github.com/cmdoret/tinycov.git
cd tinycov
pip install .
```
### Input
Only a [BAM](https://www.htslib.org/) file alignment is required as input. If it is not coordinate-sorted, tinycov will make a sorted copy named `input.sorted.bam` if the file is named `input.bam`.
### Output
If no output is provided, the coverage plot will be displayed interactively using matplotlib. If `--out` is used, the plot will be saved in a format determined by the output file's extension.
Additionally, if `--text` is provided, an output text file will be saved in the [bedgraph](https://genome.ucsc.edu/goldenPath/help/bedgraph.html) format with overlapping windows (depending on the values of `--res` and `--skip`).
### Usage
The `tinycov` commands can be invoked from the command line to list subcommands.
```
Usage: tinycov [OPTIONS] COMMAND [ARGS]...
tinycov: visualisation of coverage from BAM files using rolling window
averages.
Options:
--version Show the version and exit.
--help Show this message and exit.
Commands:
covhist Visualise the histogram of coverage in rolling windows.
covplot Visualise coverage in rolling windows, optionally save results
to...
```
The covplot subcommand plots the coverage in sliding windows along the genome. A bedgraph file with the coverage of each window can be generated using the `--text` option.
```
Usage: tinycov covplot [OPTIONS] BAM
Visualise coverage in rolling windows, optionally save results to a
bedgraph file.
Options:
-N, --no-filter Use all reads. By default, PCR duplicates and
secondary alignments are excluded
-m, --max-depth INTEGER Maximum read depth permitted. Position with higher
coverage will set to this value
-o, --out PATH Output file where to write the plot. If not
provided, the plot is shown interactively
-w, --whitelist TEXT Only include those chromosomes in the plot. List of
comma-separated chromosome names.
-b, --blacklist TEXT Exclude those chromosomes from the plot. List of
comma-separated chromosome names.
-n, --name TEXT Name of the sample (plot title). Base name of input
file by default
-B, --bins TEXT Tab-separated file of three columns (chromosome,
start, end) without header containing a custom
binning to use. Overrides --res and --skip,
optional.
-s, --skip INTEGER Stride between windows, in basepairs. [default:
1000]
-r, --res INTEGER Size of windows in which to compute coverage, in
basepairs. [default: 10000]
-t, --text PATH Output file where to write the raw data table.
-p, --ploidy INTEGER Ploidy of input sample, used to estimate coverage
threshold for aneuploidies. Setting to 0 disables
estimations.
--version Show the version and exit.
--help Show this message and exit.
```
The covhist subcommands generates a histogram of coverage values by window. To get a histogram of coverage by basepair, just set `--res` to 1.
```
Usage: tinycov covhist [OPTIONS] BAM
Visualise the histogram of coverage in rolling windows.
Options:
-N, --no-filter Use all reads. By default, PCR duplicates and
secondary alignments are excluded
-m, --max-depth INTEGER Maximum read depth permitted. Position with higher
coverage will set to this value
-o, --out PATH Output file where to write the plot. If not
provided, the plot is shown interactively
-w, --whitelist TEXT Only include those chromosomes in the plot. List of
comma-separated chromosome names.
-b, --blacklist TEXT Exclude those chromosomes from the plot. List of
comma-separated chromosome names.
-n, --name TEXT Name of the sample (plot title). Base name of input
file by default
-B, --bins TEXT Tab-separated file of three columns (chromosome,
start, end) without header containing a custom
binning to use. Overrides --res and --skip,
optional.
-s, --skip INTEGER Stride between windows, in basepairs. [default:
1000]
-r, --res INTEGER Size of windows in which to compute coverage, in
basepairs. [default: 10000]
--version Show the version and exit.
--help Show this message and exit.
```