{ "info": { "author": "Ben Weisburd", "author_email": "weisburd@broadinstitute.org", "bugtrack_url": null, "classifiers": [ "Development Status :: 4 - Beta", "Intended Audience :: Developers", "License :: OSI Approved :: MIT License", "Natural Language :: English", "Programming Language :: Python :: 2", "Programming Language :: Python :: 2.7", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.2", "Programming Language :: Python :: 3.3", "Programming Language :: Python :: 3.4", "Programming Language :: Python :: Implementation :: CPython", "Programming Language :: Python :: Implementation :: PyPy" ], "description": "Overview\n~~~~~~~~\n\nPython interface to IGV - inspired by an IGV_plotter tool originally written by `@tmfromer `_.\n\nIt includes the following executables:\n\n* :code:`igv` Launches IGV from the command line and optionally makes it load some file(s) and jump to some locus. \n* :code:`igv_plotter` Automates taking IGV screenshots of one or more data files at one or more loci.\n* :code:`igvweb_viewer` Allows bam, vcf, and/or bed file tracks to be viewed in a web browser using `igv.js `_.\n\n\nInstall\n~~~~~~~~\n\n* To install for all users, run: \n :code:`pip install igv_plotter` \n\n* 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:\n :code:`pip install igv_plotter --user` \n\n\nRun\n~~~\n\nTo see all command line options, you can do:\n\n:code:`igvweb_viewer -h`\n\n:code:`igv_plotter -h`\n\n:code:`igv -h`\n\n**igvweb_viewer script** - usage example:\n\nThis starts a webserver for viewing 3 files at 2 loci:\n\n:code:`igvweb_viewer my_file1.vcf my_file2.bam my_file3.bed 1:12345 chrX:12345`\n\nAfter starting this script, open your web browser to 127.0.0.1:8000 for an interactive\nbrowser-based IGV view of these files.\n\n**igv_plotter script** - usage example:\n\nThis loads 3 files, and takes 2 snapshots:\n\n:code:`igv_plotter my_file1.vcf my_file2.bam my_file3.bed 1:12345 chrX:12345`\n\n**igv script** - usage example:\n\nThis launches IGV with 2 files loaded at locus 1:12345:\n\n:code:`igv my_file1.vcf my_file3.bed 1:12345`\n\n\nConfigure\n~~~~~~~~~\n\nAn :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:\n:code:` = `\n\n\nContribute\n~~~~~~~~~~\n\n.. image:: https://travis-ci.org/macarthur-lab/igv_utils.svg?branch=master\n :target: https://travis-ci.org/macarthur-lab/igv_utils\n \n\nIssue reporting and pull requests are appreciated.\n\nUnit tests can be run with:\n\n:code:`python setup.py test`\n\n \nThis code is open sourced under the MIT license. \n\n\n\n", "description_content_type": null, "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/macarthur-lab/igv_utils", "keywords": "IGV", "license": "MIT", "maintainer": "", 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