Metadata-Version: 2.1
Name: bedparse
Version: 0.2.3
Summary: A simple library and CLI tool to manipulate BED files
Home-page: https://github.com/tleonardi/bedparse
Author: Tommaso Leonardi
Author-email: tom@tleo.io
License: MIT
Description: [![Build Status](https://travis-ci.org/tleonardi/bedparse.svg?branch=master)](https://travis-ci.org/tleonardi/bedparse)
        [![Docs Status](https://readthedocs.org/projects/bedparse/badge/?version=latest&style=flat)](https://bedparse.readthedocs.io/en/latest/)
        [![JOSS Status](http://joss.theoj.org/papers/22763a3b37fde13e548e884edd3221fa/status.svg)](http://joss.theoj.org/papers/22763a3b37fde13e548e884edd3221fa)
        [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2578820.svg)](https://doi.org/10.5281/zenodo.2578820)
        [![License: MIT](https://img.shields.io/badge/License-MIT-brightgreen.svg)](https://opensource.org/licenses/MIT)
        # Bedparse
        
        ![](docs/bedparse.svg)
        
        Bedparse is a simple python module and CLI tool to perform common operations on BED files.
        
        It offers 11 sub-commands that implement the following functionality:
        * `filter`: Filtering of transcripts based on annotations
        * `join`: Joining of annotation files based on transcript names
        * `gtf2bed`: Conversion from GTF to BED format
        * `convertChr`: Conversion from UCSC to Ensembl chromosome names (and viceversa)
        * `bed12tobed6`: Conversion from bed12 to bed6
        * `promoter`: Promoter reporting
        * `introns`: Intron reporting
        * `cds`: CDS reporting
        * `3pUTR` and `5pUTR`: UTR reporting 
        * `validateFormat`: Check that the file conforms with the BED format
        
        ## Installation
        
        Installing is as simple as:
        
        ```
        pip install bedparse
        ```
        
        ## Basic usage
        
        The basic syntax in the form: `bedparse subcommand [parameters]`.
        
        For a list of all subcommands and a brief explanation of what they do, use: `bedparse --help`.
        
        For a detailed explanation of each subcommand and a list of its parameters, use the `--help` option after the subcommand's name, e.g.: `bedparse promoter --help`
        
        ## Documentation
        
        Our documentation is hosted on [Read the Docs](https://bedparse.readthedocs.io/en/latest/).
        
        We also have a short [tutorial](https://bedparse.readthedocs.io/en/latest/Tutorial.html) to guide you through the basic functions.
        
        
        ## Publications
        
        If you use bedparse please cite the following [paper](https://joss.theoj.org/papers/10.21105/joss.01228):
        
        _Leonardi, (2019). Bedparse: feature extraction from BED files. Journal of Open Source Software, 4(34), 1228, https://doi.org/10.21105/joss.01228_
        
        
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Requires-Python: >=3.4
Description-Content-Type: text/markdown
