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        "author": "Yuichi Shiraishi",
        "author_email": "friend1ws@gamil.com",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 4 - Beta",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
            "Operating System :: Unix",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: 3.7",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
        ],
        "description": "# annot_utils\n\n[![Build Status](https://travis-ci.org/friend1ws/annot_utils.svg?branch=master)](https://travis-ci.org/friend1ws/annot_utils)\n[![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)\n[![PyPI](https://img.shields.io/pypi/v/annot-utils.svg?)](https://pypi.python.org/pypi/annot-utils)\n\n## Introduction\n`annot_utils` is a software for generating tabix-indexed annotation files, which can be shared by other softwares by Y.S.\nCurrently, this software support only annotatioin files for hg19 (GRCh37), hg38 (GRCh38) and mm10 (GRCm38).\n\n## Dependency\n\n### Python packages\n\n`pkg_resources`\n\n## Software\n\n[hstlib](http://www.htslib.org)\n\n## Install\n\n``annot_utils`` is available through pypi. \nTo install, type:\n```\npip install annot_utils \n```\nWhen you are not the root user, you may want to type:\n```\npip install annot_utils --user\n```\n\nAlternatively, install from the source code:\n```\nwget https://github.com/friend1ws/annot_utils/archive/v0.3.0.tar.gz\ntar xzvf v0.3.0.tar.gz \ncd annot_utils-0.3.0\npython setup.py build install --user\n```\n\nThis package has been tested on Python 2.7, 3.5, 3.6.\n\n## Update databse\nCurrently, `annot_utils` already store annotation files from [UCSC genome browser](https://genome.ucsc.edu) and several other sources upon installation.\nIf you want to update the annotation files:\n```\ncd annot_utils/resource\nbash prep_data.sh\n```\nThen, install the software from the source code.\n\n## Commands\n\n### gene\n\nGenerate gene annotation bed flies indexed by tabix.\n\n```\nannot_utils gene [-h] \n                 [--gene_model {refseq,gencode}] [--grc]\n                 [--genome_id {hg19,hg38,mm10}] [--add_ref_id]\n                 gene.bed.gz\n```\n\n\n### exon\n\nGenerate exon annotation bed flies indexed by tabix.\n\n\n```\nannot_utils exon [-h] \n                 [--gene_model {refseq,gencode}] [--grc]\n                 [--genome_id {hg19,hg38,mm10}] [--add_ref_id]\n                 exon.bed.gz\n```\n\n\n### coding\n\nGenerate regional (coding, intronic, 5'UTR, 3'UTR and so on) annotation bed flies indexed by tabix.\n\n```\nannot_utils coding [-h] \n                   [--gene_model {refseq,gencode}] [--grc]\n                   [--genome_id {hg19,hg38,mm10}] [--add_ref_id]\n                   coding.bed.gz\n```\n\n### junction\n\nGenerate annotated splicing junction bed files indexed by tabix.\n\n```\nannot_utils junction\nusage: annot_utils junction [-h] \n \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0  [--gene_model {refseq,gencode}] [--grc]\n                            [--genome_id {hg19,hg38,mm10}] [--add_ref_id]\n \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0junction.bed.gz\n```\n\n### boundary\n\n\nGenerate exon intron boundary annotation files index by tabix.\n\n```\nannot_utils boundary [-h] \n                     [--genome_id {hg19,hg38,mm10}] [--grc]\n                     [--donor_size donor_size]\n                     [--acceptor_size acceptor_size]\n                     boudary.bed.gz\n```",
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