Metadata-Version: 2.1
Name: tinycov
Version: 0.0.8
Summary: Standalone command line tool to visualize coverage from a BAM file
Home-page: https://github.com/cmdoret/tinycov
Author: cmdoret
Author-email: cyril.matthey-doret@pasteur.fr
License: MIT
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Visualization
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX
Classifier: Operating System :: Unix
Classifier: Operating System :: MacOS
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Requires-Dist: pandas
Requires-Dist: numpy
Requires-Dist: matplotlib
Requires-Dist: seaborn
Requires-Dist: pysam
Requires-Dist: click

### tinycov
[![PyPI version](https://badge.fury.io/py/tinycov.svg)](https://badge.fury.io/py/tinycov) [![Build Status](https://travis-ci.com/cmdoret/tinycov.svg?branch=master)](https://travis-ci.com/cmdoret/tinycov) [![codecov](https://codecov.io/gh/cmdoret/tinycov/branch/master/graph/badge.svg)](https://codecov.io/gh/cmdoret/tinycov) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](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

```
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.

```


