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Standalone command line tool to visualize coverage from a BAM file

Project description

tinycov

PyPI version Build Status codecov Language grade: Python Code style: 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.

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 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 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.

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