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Standalone command line tool to visualize coverage from a BAM file

Project description

tinycov

PyPI version Build Status codecov 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

Usage: tinycov.py [OPTIONS] BAM

Options:
  -r, --res INTEGER     Size of windows in which to compute coverage, in
                        basepairs.  [default: 10000]
  -s, --skip INTEGER    Stride between windows, in basepairs.  [default: 1000]
  -n, --name TEXT       Name of the sample (plot title). Base name of input
                        file by default
  -b, --blacklist TEXT  Exclude those chromosomes from the plot. List of
                        comma-separated chromosome names.
  -w, --whitelist TEXT  Only include those chromosomes in the plot. List of
                        comma-separated chromosome names.
  -o, --out PATH        Output file where to write the plot. If not provided,
                        the plot is shown interactively
  -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
  --help                Show this message and exit.

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