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        "author": "Yuichi Shiraishi",
        "author_email": "friend1ws@gamil.com",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 3 - Alpha",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
            "Operating System :: Unix",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "# junc_utils\n\n[![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)\n[![Build Status](https://travis-ci.org/friend1ws/junc_utils.svg?branch=devel)](https://travis-ci.org/friend1ws/junc_utils)\n\nUtility functions for analyzing splicing junction (generated by STAR, .SJ.out.tab files)\n\n## Dependency\n\n### Python\npysam, [annot_utils](https://github.com/friend1ws/annot_utils) packages.\n\n### Software\n[htslib](http://www.htslib.org), [bedtools](http://bedtools.readthedocs.io/en/latest/)\n\n## Install\n\n```\npip install junc_utils\n```\n\nAlternatively, you can install from the source code\n```\nwget https://github.com/friend1ws/junc_utils/archive/v0.4.0.tar.gz\ntar zxvf v0.4.0.tar.gz\ncd junc_utils-0.4.0\npython setup.py build install\n```\n\nThis package has been tested on Python 2.7, 3.5, 3.6.\n\n## Commands\n\n### fitler\n\nfilter out splicing junctions outside specified conditions\n```\njunc_utils filter [-h] [--read_num_thres READ_NUM_THRES]\n                         [--overhang_thres OVERHANG_THRES] [--keep_annotated]\n                         [--pooled_control_file POOLED_CONTROL_FILE]\n                         sample.SJ.out.tab output.txt\n```\n\n### annotate\n\nannotate splicing junctions\n\n```\njunc_utils annotate [-h] [--grc] [--genome_id {hg19,hg38,mm10}]\n                           [--junction_margin JUNCTION_MARGIN]\n                           [--exon_margin EXON_MARGIN]\n                           sample.SJ.out.tab output.txt\n```\n\n### merge_control\n\nmerge, compress and index the splicing junction list\n\n```\njunc_utils merge_control [-h] [--read_num_thres READ_NUM_THRES]\n                                [--overhang_thres OVERHANG_THRES]\n                                [--keep_annotated]\n                                [--sample_num_thres SAMPLE_NUM_THRES]\n                                junc_list.txt output_path\n```\n\n### associate\n\nassociate junctions with mutations or SVs\n\n```\njunc_utils associate [-h] [--grc] [--genome_id {hg19,hg38,mm10}]\n                            [--donor_size donor_size]\n                            [--acceptor_size acceptor_size]\n                            [--reference reference.fa] [--debug]\n                            [--mutation_format {vcf,anno}] [--only_dist]\n                            [--only_dist_search_margin only_dist_search_margin]\n                            [--sv] [--branchpoint]\n                            [--branchpoint_size branchpoint_size]\n                            annotated_junction.SJ.out.tab mutation.vcf.gz\n                            output_file\n```",
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