Metadata-Version: 2.1
Name: tinycov
Version: 0.3.1
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
Description: ### 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) [![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/cmdoret/tinycov.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/cmdoret/tinycov/context:python) [![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
        
        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.
        ```
        
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
