Metadata-Version: 1.1
Name: igv_plotter
Version: 0.9.8.7
Summary: python interface to IGV that simplifies creating screenshots of BAMs, VCFs, BEDs, etc for one-off spot checking or automated / scripted image collection
Home-page: https://github.com/macarthur-lab/igv_utils
Author: Ben Weisburd
Author-email: weisburd@broadinstitute.org
License: MIT
Description: Overview
        ~~~~~~~~
        
        Python interface to IGV - inspired by an IGV_plotter tool originally written by `@tmfromer <https://github.com/tmfromer>`_.
        
        It includes the following executables:
        
        * :code:`igv`    Launches IGV from the command line and optionally makes it load some file(s) and jump to some locus. 
        * :code:`igv_plotter`   Automates taking IGV screenshots of one or more data files at one or more loci.
        * :code:`igvweb_viewer`  Allows bam, vcf, and/or bed file tracks to be viewed in a web browser using `igv.js <https://github.com/jrobinso>`_.
        
        
        Install
        ~~~~~~~~
        
        * To install for all users, run:   
          :code:`pip install igv_plotter`   
        
        * To install in your home directory (eg. if you don't have permissions to install for all users), add ~/.local/bin to your PATH and run:
          :code:`pip install igv_plotter --user` 
        
        
        Run
        ~~~
        
        To see all command line options, you can do:
        
        :code:`igvweb_viewer -h`
        
        :code:`igv_plotter -h`
        
        :code:`igv -h`
        
        **igvweb_viewer script** - usage example:
        
        This starts a webserver for viewing 3 files at 2 loci:
        
        :code:`igvweb_viewer my_file1.vcf  my_file2.bam  my_file3.bed 1:12345 chrX:12345`
        
        After starting this script, open your web browser to 127.0.0.1:8000 for an interactive
        browser-based IGV view of these files.
        
        **igv_plotter script** - usage example:
        
        This loads 3 files, and takes 2 snapshots:
        
        :code:`igv_plotter  my_file1.vcf  my_file2.bam  my_file3.bed 1:12345 chrX:12345`
        
        **igv script** - usage example:
        
        This launches IGV with 2 files loaded at locus 1:12345:
        
        :code:`igv  my_file1.vcf  my_file3.bed 1:12345`
        
        
        Configure
        ~~~~~~~~~
        
        An :code:`~/.igv_plotter` config file can be created and used to persitantly set any :code:`igv_plotter` or :code:`igv` command line options, by using lines like:
        :code:`<command line option (without --)> = <value>`
        
        
        Contribute
        ~~~~~~~~~~
        
        .. image:: https://travis-ci.org/macarthur-lab/igv_utils.svg?branch=master
           :target: https://travis-ci.org/macarthur-lab/igv_utils
            
        
        Issue reporting and pull requests are appreciated.
        
        Unit tests can be run with:
        
        :code:`python setup.py test`
        
            
        This code is open sourced under the MIT license. 
        
        
        
        
Keywords: IGV,snapshots,screenshots,images,BAM,VCF,bioinformatics,sequencing,NGS,variants
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.2
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Programming Language :: Python :: Implementation :: PyPy
