{
    "info": {
        "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 :: 3.6",
            "Programming Language :: Python :: 3.7",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
        ],
        "description": "# intron_retention_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/intron_retention_utils.svg?branch=devel)](https://travis-ci.org/friend1ws/intron_retention_utils)\n\nA software for calculating intron retention events genome-wide from RNA sequencing data.\n\n## Dependency\n\n### Python\n\n`pysam>=0.9.0`,[`annot_utils>=0.3.0`](https://github.com/friend1ws/annot_utils) packages.\n\n### Software\n\n[bedtools](http://bedtools.readthedocs.io/en/latest/), [hstlib](http://www.htslib.org)\n\n## Install \n\n```\npip install intron_retention_utils\n```\n\nAlternatively, you can install from the source code.\n```\ngit clone  https://github.com/friend1ws/intron_retention_util.git\ncd intron_retention_utils\npython setup.py build install\n```\n\nThis package has been tested on Python 2.7, 3.5, 3.6.\n\n## Preparation\n\nFor **allele_count** command, a [Smith-Waterman shared library](https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library) from Mengyao Zhao is necessary.\nAlso, if your BAM file is aligned to reference genome using name convention other than UCSC,\nCreate the `libssw.so` and add the path to the LD_LIBRARY_PATH environment variable.\n\n## Commands\n\n### simple_count\n\nSimple intron retention count program.\nCalculate the number of reads covering each exon-intron boundary and \nputative intron retention reads (that covering enlarged reagion by specified margin size (e.g. -5bp and +5bp from that boundary).\n\n```\nintron_retention_utils simple_count [-h] \n \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0  [--grc]\n                                    [--genome_id {hg19,hg38,mm10}]\n                                    [--intron_retention_check_size intron_retention_check_size]\n                                    [--mapping_qual_thres mapping_qual_thres]\n                                    [--keep_improper_pair] [--debug]\n                                    sequence.bam output_file\n```\n\n#### About result\n\n* **Chr**: chromosome of the exon-intron boundary\n* **Boundary_Pos**: coordinate of the exon-intron boundary (the last exonic base)\n* **Gene_Symbol**: gene symbol from refGene.txt.gz\n* **Motif_Type**: splicing donor or acceptor\n* **Strand**: transcription starnd of the gene\n* **Junction_List**: cannonical splicing junction list from that exon-intron boundary\n* **Gene_ID_List**: refGene ID list with that exon-intron boundary\n* **Exon_Num_List**: exon numbers for each refGene IDs\n* **Edge_Read_Count**: the number of reads covering each exon-intron boundary\n* **Intron_Retention_Read_Count**: the number of putative intron retention reads\n\n\n\n### allele_count\n\n```\nintron_retention_utils allele_count [-h] \n \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0  [--grc]\n                                    [--genome_id {hg19,hg38,mm10}]\n                                    [--donor_size donor_size]\n                                    [--acceptor_size acceptor_size]\n                                    [--template_size check_size]\n                                    [--template_score_margin check_size]\n                                    [--read_search_margin read_search_margin]\n                                    [--debug]\n                                    sequence.bam mutation.txt\n                                    output.txt reference.fa\n```\n\n#### About result\n\n* **Gene_Symbol**: gene symbol\n* **Chr_Mut**: chromosome of the mutation\n* **Start_Mut**: start coordinate of the mutation\n* **End_Mut**: end coordinate of the the mutation\n* **Ref_Mut**: reference allele of the mutation\n* **Alt_Mut**: alternative allele of the mutation\n* **Chr_Motif**: chromosome of the splicing motif\n* **Start_Motif**: start coordinate of the splicing motif\n* **End_Motif**: end coordinate of the splicing motif\n* **Type_Motif**: donor or acceptor\n* **Strand_Motif**: transcription strand of the gene \n* **Splice_Junction_Negative**: the number of normaly spliced reads without the alternative allele\n* **Splice_Junction_Positive**: the number of normaly spliced reads with the alternative allele\n* **Intron_Retention_Negative**: the number of putative intron retention reads without the alternative allele\n* **Intron_Retention_Positive**: the number of putative intron retention reads with the alternative allele\n\n### merge_control\n\nMerge the intron retention file of control data (typically) for later filtering.\n\n```\nintron_retention_utils merge_control [-h] \n \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 [--ratio_thres RATIO_THRES]\n                                     [--sample_num_thres SAMPLE_NUM_THRES]\n                                     intron_retention_list.txt\n                                     output_file\n```\n\n### filter\n\nFilter out intron retentions that do not satisty specified conditions\n```\nintron_retention_utils filter [-h] \n \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0  [--num_thres NUM_THRES]\n                              [--ratio_thres RATIO_THRES]\n                              [--pooled_control_file POOLED_CONTROL_FILE]\n                              intron_retention.txt output.txt\n```\n\n### associate\n\nAssociate intron retention counts (typically output of simple_count commands) with mutations\n```\nintron_retention_utils associate [-h] [--donor_size donor_size]\n                                        [--acceptor_size acceptor_size]\n                                        [--mutation_format {vcf,anno}]\n                                        [--reference reference.fa] [--sv]\n                                        [--intron_margin intron_margin]\n                                        [--debug]\n                                        intron_retention.txt mutation.txt\n                                        output_file\n```\n\n#### About result\nThe following columns are added to the input files:\n\n* **Mutation_Key**: vcf format mutation aggregated by commas\n* **Motif_Pos**: coordinate of motif positions\n* **Mutation_Type**: `splicing donor disruption` or `splicing acceptor disruption`\n* **Is_Canonical**: whether the mutation is disrupting cannonical splicing motifs (GT-AG) or not\n* **Intron_Retention_Type**: `direct-impact` or `opposite-side-impact`",
        "description_content_type": "text/markdown",
        "docs_url": null,
        "download_url": "",
        "downloads": {
            "last_day": -1,
            "last_month": -1,
            "last_week": -1
        },
        "home_page": "https://github.com/friend1ws/intron_retention_utils",
        "keywords": "",
        "license": "GPLv3",
        "maintainer": "",
        "maintainer_email": "",
        "name": "intron-retention-utils",
        "package_url": "https://pypi.org/project/intron-retention-utils/",
        "platform": "",
        "project_url": "https://pypi.org/project/intron-retention-utils/",
        "project_urls": {
            "Homepage": "https://github.com/friend1ws/intron_retention_utils"
        },
        "release_url": "https://pypi.org/project/intron-retention-utils/0.6.3/",
        "requires_dist": null,
        "requires_python": "",
        "summary": "Python tools for extracting intron retention events",
        "version": "0.6.3"
    },
    "last_serial": 5882359,
    "releases": {
        "0.4.0": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "c29fc7d2e11170003615251ec9a25595",
                    "sha256": "e6d463dad4a25153d0fef0f9a7c520338d69248a99045c4291e4d4fb6be6a833"
                },
                "downloads": -1,
                "filename": "intron_retention_utils-0.4.0.tar.gz",
                "has_sig": false,
                "md5_digest": "c29fc7d2e11170003615251ec9a25595",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 20522,
                "upload_time": "2018-01-31T04:02:47",
                "url": "https://files.pythonhosted.org/packages/76/e5/f9ed29b48aa352fd06c8ebe927454d2ebcd7c169ce76cdc2928daa16e9d5/intron_retention_utils-0.4.0.tar.gz"
            }
        ],
        "0.4.0rc1": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "4ca0d7f058fdf45f2226c3656a90b83f",
                    "sha256": "b30eaf560748f908fbe5a4c4e25c77f4f2a89317204543c4f281886f3cce0768"
                },
                "downloads": -1,
                "filename": "intron_retention_utils-0.4.0rc1.tar.gz",
                "has_sig": false,
                "md5_digest": "4ca0d7f058fdf45f2226c3656a90b83f",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 20530,
                "upload_time": "2018-01-13T01:09:31",
                "url": "https://files.pythonhosted.org/packages/72/64/ee9aa6d71ecc369fedda8c903d68611d814997dffc3d7394baf02190d27d/intron_retention_utils-0.4.0rc1.tar.gz"
            }
        ],
        "0.5.0": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "b073eda779e077321abe5e603a6d31e5",
                    "sha256": "ed24b92cde9c339c2d253f80ef3b98e2898b1ce7341c41e485b4db4d3e244b5b"
                },
                "downloads": -1,
                "filename": "intron_retention_utils-0.5.0.tar.gz",
                "has_sig": false,
                "md5_digest": "b073eda779e077321abe5e603a6d31e5",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 20666,
                "upload_time": "2018-03-10T00:51:33",
                "url": "https://files.pythonhosted.org/packages/4b/d9/77860217afcf537a476cec6214bfea012ea550e7691f72d1a847eec3a7f0/intron_retention_utils-0.5.0.tar.gz"
            }
        ],
        "0.5.1": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "6d7d56e36b51a539ef9362a72384d6be",
                    "sha256": "aaedb77abffa081a0ae601a62457461ac36b261e5c4e5a7ab53f3b8c15f7ac3b"
                },
                "downloads": -1,
                "filename": "intron_retention_utils-0.5.1.tar.gz",
                "has_sig": false,
                "md5_digest": "6d7d56e36b51a539ef9362a72384d6be",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 21066,
                "upload_time": "2018-03-12T17:42:30",
                "url": "https://files.pythonhosted.org/packages/cf/e6/4f688a0914cdeb0109d1635b5f645124d4108ceab671b8681c34846690d3/intron_retention_utils-0.5.1.tar.gz"
            }
        ],
        "0.6.0": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "9afc1dd0accd0d2e153155bc3c989d9d",
                    "sha256": "9d0b2a335f4e041a18d12a2d602668cf3a51be8825f2a21081cae003022bf7ee"
                },
                "downloads": -1,
                "filename": "intron_retention_utils-0.6.0.tar.gz",
                "has_sig": false,
                "md5_digest": "9afc1dd0accd0d2e153155bc3c989d9d",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 24060,
                "upload_time": "2019-05-18T06:45:46",
                "url": "https://files.pythonhosted.org/packages/5e/10/b1c64a7491947a75b6b998f2ecf63ea51b774051798b8deb700e07d8d4f7/intron_retention_utils-0.6.0.tar.gz"
            }
        ],
        "0.6.0b1": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "63fecd30a4fbf244213a277bf2d74e65",
                    "sha256": "5e47575fb283755ff47e1f1f6873cd12a37a73917daa29e585437b5351e3ce04"
                },
                "downloads": -1,
                "filename": "intron_retention_utils-0.6.0b1.tar.gz",
                "has_sig": false,
                "md5_digest": "63fecd30a4fbf244213a277bf2d74e65",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 21833,
                "upload_time": "2019-05-18T03:38:21",
                "url": "https://files.pythonhosted.org/packages/d8/94/c18fbddd6ada6a34356db83e7388aecda741292965f8c36072678c9d77fc/intron_retention_utils-0.6.0b1.tar.gz"
            }
        ],
        "0.6.0rc1": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "b281663683b2ff6498ec780e1bb43495",
                    "sha256": "13789987b9d6781c5a1b501605e23acdd29891acddf5ab64a7b9150152a67c4a"
                },
                "downloads": -1,
                "filename": "intron_retention_utils-0.6.0rc1.tar.gz",
                "has_sig": false,
                "md5_digest": "b281663683b2ff6498ec780e1bb43495",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 24023,
                "upload_time": "2019-05-18T06:25:19",
                "url": "https://files.pythonhosted.org/packages/9a/9b/ce69a78f3d12b293a4678cd186e3517e709ff815a9e288f950c0ad143e5e/intron_retention_utils-0.6.0rc1.tar.gz"
            }
        ],
        "0.6.1": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "3449799a2961c5438fb93f4247d3a8ad",
                    "sha256": "01c5d36d88f993125fe913c5eaedef295dfbdef00043efb92d31e4badc78776b"
                },
                "downloads": -1,
                "filename": "intron_retention_utils-0.6.1.tar.gz",
                "has_sig": false,
                "md5_digest": "3449799a2961c5438fb93f4247d3a8ad",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 24249,
                "upload_time": "2019-08-31T03:50:48",
                "url": "https://files.pythonhosted.org/packages/13/30/49065ec0574110088681439c237e9fb45894fdbccc6a8130a27e1dcb6ba8/intron_retention_utils-0.6.1.tar.gz"
            }
        ],
        "0.6.2": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "76e57fb1d2f5b43dc65eb6142c672610",
                    "sha256": "f06d35aa57aa8758f06a11170a1ed0c8eed093e64bfe0cc109c7a6e9b77e507b"
                },
                "downloads": -1,
                "filename": "intron_retention_utils-0.6.2.tar.gz",
                "has_sig": false,
                "md5_digest": "76e57fb1d2f5b43dc65eb6142c672610",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 24955,
                "upload_time": "2019-09-06T21:16:14",
                "url": "https://files.pythonhosted.org/packages/8a/01/309e16f75439856965ae6b48ad9ce1131e76314a91987b47827bdc70d54d/intron_retention_utils-0.6.2.tar.gz"
            }
        ],
        "0.6.3": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "04feb1d567c4e50c96cf92d085752f73",
                    "sha256": "a64f2cc79e82b7ab6210c6ddd1e4ab8e3890bd2b1d6f5f4a9e4778db1935b453"
                },
                "downloads": -1,
                "filename": "intron_retention_utils-0.6.3.tar.gz",
                "has_sig": false,
                "md5_digest": "04feb1d567c4e50c96cf92d085752f73",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 25064,
                "upload_time": "2019-09-24T23:47:57",
                "url": "https://files.pythonhosted.org/packages/53/45/e8b753d19a3630049c94fde4ee8144e30de237cb2ee3c668669b968e8914/intron_retention_utils-0.6.3.tar.gz"
            }
        ]
    },
    "urls": [
        {
            "comment_text": "",
            "digests": {
                "md5": "04feb1d567c4e50c96cf92d085752f73",
                "sha256": "a64f2cc79e82b7ab6210c6ddd1e4ab8e3890bd2b1d6f5f4a9e4778db1935b453"
            },
            "downloads": -1,
            "filename": "intron_retention_utils-0.6.3.tar.gz",
            "has_sig": false,
            "md5_digest": "04feb1d567c4e50c96cf92d085752f73",
            "packagetype": "sdist",
            "python_version": "source",
            "requires_python": null,
            "size": 25064,
            "upload_time": "2019-09-24T23:47:57",
            "url": "https://files.pythonhosted.org/packages/53/45/e8b753d19a3630049c94fde4ee8144e30de237cb2ee3c668669b968e8914/intron_retention_utils-0.6.3.tar.gz"
        }
    ]
}