{
    "info": {
        "author": "Forest Dussault",
        "author_email": "forest.dussault@canada.ca",
        "bugtrack_url": null,
        "classifiers": [],
        "description": "# seqPresenceAbsence\n\n### Requirements\n- Python >= 3.6\n- Perl 5 (required for FASconCAT-G)\n- [ncbi-blast+](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download) (makeblastdb and blastn must be in your $PATH)\n- [MUSCLE](https://www.drive5.com/muscle/) (muscle must be in your $PATH)\n\n### Installation\n```\npip install seqPresenceAbsence\n```\n\n### Usage\n```\nUsage: seqPresenceAbsence [OPTIONS]\n\n  seqPresenceAbsence is a simple script for querying an input nucleotide\n  FASTA file against a database of sequences. Will return an .xlsx and .csv\n  report of presence/absence of the sequences. Version: 0.2.0.\n\nOptions:\n  -i, --indir PATH           Path to directory containing FASTA files you want\n                             to query  [required]\n  -t, --targets PATH         Path to multi-FASTA containing targets of\n                             interest  [required]\n  -o, --outdir PATH          Root directory to store all output files\n                             [required]\n  -p, --perc_identity FLOAT  Equivalent to the -perc_identity argument in\n                             blastn. Defaults to 95.00.\n  -k, --keep_db_seqs         Set this flag to keep the target sequence in\n                             addition to the query sequence from BLAST.\n  -v, --verbose              Set this flag to enable more verbose logging.\n  --version                  Specify this flag to print the version and exit.\n  --help                     Show this message and exit.\n```\n\n### Notes\nThis package includes a distribution of FASconCAT-G v1.04, developed by Patrick K\u00fcck.\n\n### References\n- K\u00fcck P., Meusemann K. (2010): FASconCAT: Convenient handling of data matrices. Mol. Phylogen. Evol. 56:1115-1118\n- Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput\n  Nucleic Acids Res. 32(5):1792-1797",
        "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/bfssi-forest-dussault/SeqPresenceAbsence",
        "keywords": "",
        "license": "",
        "maintainer": "",
        "maintainer_email": "",
        "name": "seqPresenceAbsence",
        "package_url": "https://pypi.org/project/seqPresenceAbsence/",
        "platform": "",
        "project_url": "https://pypi.org/project/seqPresenceAbsence/",
        "project_urls": {
            "Homepage": "https://github.com/bfssi-forest-dussault/SeqPresenceAbsence"
        },
        "release_url": "https://pypi.org/project/seqPresenceAbsence/0.2.2/",
        "requires_dist": null,
        "requires_python": "~=3.6",
        "summary": "Package for checking for the presence/absence of markers against a set of samples",
        "version": "0.2.2"
    },
    "last_serial": 4704295,
    "releases": {
        "0.0.1": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "71754181ddd99704a91b495223c7e100",
                    "sha256": "dac27e6f9c00141c279ee9774e4aaffa9396e1b1b25f4bb963bc4dbf7bcd480c"
                },
                "downloads": -1,
                "filename": "seqPresenceAbsence-0.0.1.tar.gz",
                "has_sig": false,
                "md5_digest": "71754181ddd99704a91b495223c7e100",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": "~=3.6",
                "size": 5326,
                "upload_time": "2018-11-20T14:33:45",
                "url": "https://files.pythonhosted.org/packages/c2/7a/3c2d5e8c861dd47f3492b1d1e91ed7462d1aa59c1ba6174c731ae6740a80/seqPresenceAbsence-0.0.1.tar.gz"
            }
        ],
        "0.0.2": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "dd1f22254f08e40a3192f400ac823e06",
                    "sha256": "88c1f1e4f352f47950f71b5e14796da3f3772d107641ed9cb074d630bbf1bcc2"
                },
                "downloads": -1,
                "filename": "seqPresenceAbsence-0.0.2.tar.gz",
                "has_sig": false,
                "md5_digest": "dd1f22254f08e40a3192f400ac823e06",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": "~=3.6",
                "size": 5666,
                "upload_time": "2018-11-20T16:49:21",
                "url": "https://files.pythonhosted.org/packages/53/29/6b9438ff2fcefa7992f68ef898afb4c55951179fe7950e1d7265cc226db2/seqPresenceAbsence-0.0.2.tar.gz"
            }
        ],
        "0.0.4": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "f5bc2b52cc46ba44b9640edc7e7d98c7",
                    "sha256": "088653a2ac8cde3c1dae9664dad2c81c1af61a661bb59417572721dc3c06525a"
                },
                "downloads": -1,
                "filename": "seqPresenceAbsence-0.0.4.tar.gz",
                "has_sig": false,
                "md5_digest": "f5bc2b52cc46ba44b9640edc7e7d98c7",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": "~=3.6",
                "size": 5781,
                "upload_time": "2018-11-20T20:06:14",
                "url": "https://files.pythonhosted.org/packages/8c/0b/f9d47332cfa6ae3edd82dc7cd125be6033ea7db9aba59a92e8d27c8021ff/seqPresenceAbsence-0.0.4.tar.gz"
            }
        ],
        "0.0.5": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "a99204d3c397eec23a9029d9466cf525",
                    "sha256": "cfa7cb70c6471d15d3ca48c62c414104847af2db00178bc9c6efca5e4630c276"
                },
                "downloads": -1,
                "filename": "seqPresenceAbsence-0.0.5.tar.gz",
                "has_sig": false,
                "md5_digest": "a99204d3c397eec23a9029d9466cf525",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": "~=3.6",
                "size": 5849,
                "upload_time": "2018-11-28T19:36:50",
                "url": "https://files.pythonhosted.org/packages/48/98/0a7c43ceff282255620a99b001af8398827d6e035c2acdf99fa570f5e076/seqPresenceAbsence-0.0.5.tar.gz"
            }
        ],
        "0.0.6": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "713bdb19f8cd7cd0afe968c3878480bc",
                    "sha256": "aafee81d6ada7dc995c0472551751713d9fc4c8d7db245ef69de65a5932aa38f"
                },
                "downloads": -1,
                "filename": "seqPresenceAbsence-0.0.6.tar.gz",
                "has_sig": false,
                "md5_digest": "713bdb19f8cd7cd0afe968c3878480bc",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": "~=3.6",
                "size": 5927,
                "upload_time": "2018-11-29T18:25:10",
                "url": "https://files.pythonhosted.org/packages/81/00/324769a4214b5fce1196abcebaae990317ed1a16f12c1d9b43580a100ae4/seqPresenceAbsence-0.0.6.tar.gz"
            }
        ],
        "0.0.7": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "588575fff783877ea71a59df46b6363d",
                    "sha256": "7319663a0246eaa36bff7e538c340252a120ef7692ea5d7545bf63b1229bb0eb"
                },
                "downloads": -1,
                "filename": "seqPresenceAbsence-0.0.7.tar.gz",
                "has_sig": false,
                "md5_digest": "588575fff783877ea71a59df46b6363d",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": "~=3.6",
                "size": 6607,
                "upload_time": "2018-11-30T18:50:02",
                "url": "https://files.pythonhosted.org/packages/68/7d/94283eb32587634d4a4ff8caa99942ca246bd529c1a7bd87985649a040b7/seqPresenceAbsence-0.0.7.tar.gz"
            }
        ],
        "0.0.8": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "6beea5af3fde7c6c566223365775992e",
                    "sha256": "f441def65b0d05aa130af7443b02788b975882ec92e8cc6e16f7dbc9d602784d"
                },
                "downloads": -1,
                "filename": "seqPresenceAbsence-0.0.8.tar.gz",
                "has_sig": false,
                "md5_digest": "6beea5af3fde7c6c566223365775992e",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": "~=3.6",
                "size": 6624,
                "upload_time": "2018-11-30T18:56:48",
                "url": "https://files.pythonhosted.org/packages/ed/9b/d4358e4b5debfb9d97f1c4c73bd5db9385f4356bf1f5f04e37e6483b053a/seqPresenceAbsence-0.0.8.tar.gz"
            }
        ],
        "0.1.0": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "afb6cd45354f82dea0e54230ba5c0dec",
                    "sha256": "3b3929905c4e4f067c854ea677a514f663fd75c5f511b7c6699bd2f8ae279a07"
                },
                "downloads": -1,
                "filename": "seqPresenceAbsence-0.1.0.tar.gz",
                "has_sig": false,
                "md5_digest": "afb6cd45354f82dea0e54230ba5c0dec",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": "~=3.6",
                "size": 6644,
                "upload_time": "2018-11-30T19:03:47",
                "url": "https://files.pythonhosted.org/packages/23/ff/b03fbe4ac6adcb9bf4231896f455c1c841976427604fb61d16e9ad2c65a0/seqPresenceAbsence-0.1.0.tar.gz"
            }
        ],
        "0.1.1": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "1adf5ee89b11afa140d09b7b0bcc2c68",
                    "sha256": "0950709c4bb513a1099edbed087904cd94aa9513cce016d884a252e426f21c44"
                },
                "downloads": -1,
                "filename": "seqPresenceAbsence-0.1.1.tar.gz",
                "has_sig": false,
                "md5_digest": "1adf5ee89b11afa140d09b7b0bcc2c68",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": "~=3.6",
                "size": 6802,
                "upload_time": "2018-12-20T18:48:15",
                "url": "https://files.pythonhosted.org/packages/d8/f2/ff14bc53a2b66412a994bf696a715c4b5dc666a0d06dd81c192c0acbf6b4/seqPresenceAbsence-0.1.1.tar.gz"
            }
        ],
        "0.1.2": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "2651b7bd0d2223ab89b2ec11f727125f",
                    "sha256": "4b4be9b886176cc257cf890b98d85e0dc910a48a1373a76a7e37f07a06679e51"
                },
                "downloads": -1,
                "filename": "seqPresenceAbsence-0.1.2.tar.gz",
                "has_sig": false,
                "md5_digest": "2651b7bd0d2223ab89b2ec11f727125f",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": "~=3.6",
                "size": 6893,
                "upload_time": "2018-12-20T20:09:59",
                "url": "https://files.pythonhosted.org/packages/c6/ed/a5c7cdcf78f3cc919adb46ebc82ac8207de11c1e0b318df4a6fc66ccb34b/seqPresenceAbsence-0.1.2.tar.gz"
            }
        ],
        "0.1.3": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "4746e91314277be6b49ead2683f73ee7",
                    "sha256": "185e9e2c14413395e424ef7fd62bf6e6e8e5696b7a894206f2bd3a0ba4a9aa9c"
                },
                "downloads": -1,
                "filename": "seqPresenceAbsence-0.1.3.tar.gz",
                "has_sig": false,
                "md5_digest": "4746e91314277be6b49ead2683f73ee7",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": "~=3.6",
                "size": 6879,
                "upload_time": "2019-01-07T13:44:52",
                "url": "https://files.pythonhosted.org/packages/d6/7e/a9ecfafc8d187bd7848e679b0aa84ee68eba7f658a8d57898068cd4cae9a/seqPresenceAbsence-0.1.3.tar.gz"
            }
        ],
        "0.1.4": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "a764485647040a2f7546b9b168fa95ff",
                    "sha256": "003c4b90817253f3d93288459b38cde3f1fb4c7370ab3bc97acf8256d44d753e"
                },
                "downloads": -1,
                "filename": "seqPresenceAbsence-0.1.4.tar.gz",
                "has_sig": false,
                "md5_digest": "a764485647040a2f7546b9b168fa95ff",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": "~=3.6",
                "size": 7131,
                "upload_time": "2019-01-08T20:29:54",
                "url": "https://files.pythonhosted.org/packages/98/3b/e0191f1c30330bb62c97d6cc56df350eec097d895614e8e52738ae6d1c2e/seqPresenceAbsence-0.1.4.tar.gz"
            }
        ],
        "0.2.0": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "155e8026bf73253370c701315b8887b1",
                    "sha256": "149f5910030230baec7f63e4345b00597defd484092c20ae3d58613d99670e97"
                },
                "downloads": -1,
                "filename": "seqPresenceAbsence-0.2.0.tar.gz",
                "has_sig": false,
                "md5_digest": "155e8026bf73253370c701315b8887b1",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": "~=3.6",
                "size": 46397,
                "upload_time": "2019-01-09T19:10:45",
                "url": "https://files.pythonhosted.org/packages/90/17/c5dea8e469c9548187ac0761bc4f893728d3916097e76f51e806222a2d3d/seqPresenceAbsence-0.2.0.tar.gz"
            }
        ],
        "0.2.1": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "9fc3b3f2418d80506bcc012f0fd53ed3",
                    "sha256": "2f82f80fd0016259d9b52f945a187b245e39ca8d08af5e8d6409718316945785"
                },
                "downloads": -1,
                "filename": "seqPresenceAbsence-0.2.1.tar.gz",
                "has_sig": false,
                "md5_digest": "9fc3b3f2418d80506bcc012f0fd53ed3",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": "~=3.6",
                "size": 46510,
                "upload_time": "2019-01-09T20:45:39",
                "url": "https://files.pythonhosted.org/packages/fa/e6/be6816897fd00ee40dd05971b20570c86e2d53f009fb89f9ea77e8788dd2/seqPresenceAbsence-0.2.1.tar.gz"
            }
        ],
        "0.2.2": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "c6c3d05877425503430e13e979b31d9d",
                    "sha256": "fa9ebd2731dcb862a0d5b30685c9b31f1418d73170c6c9767fc5a9da8ac40885"
                },
                "downloads": -1,
                "filename": "seqPresenceAbsence-0.2.2.tar.gz",
                "has_sig": false,
                "md5_digest": "c6c3d05877425503430e13e979b31d9d",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": "~=3.6",
                "size": 46082,
                "upload_time": "2019-01-16T17:18:37",
                "url": "https://files.pythonhosted.org/packages/55/56/7f6b9dcb85c31c7e1775cc8fbb8703bcccf1df56d79629e23e1ff977b0b2/seqPresenceAbsence-0.2.2.tar.gz"
            }
        ]
    },
    "urls": [
        {
            "comment_text": "",
            "digests": {
                "md5": "c6c3d05877425503430e13e979b31d9d",
                "sha256": "fa9ebd2731dcb862a0d5b30685c9b31f1418d73170c6c9767fc5a9da8ac40885"
            },
            "downloads": -1,
            "filename": "seqPresenceAbsence-0.2.2.tar.gz",
            "has_sig": false,
            "md5_digest": "c6c3d05877425503430e13e979b31d9d",
            "packagetype": "sdist",
            "python_version": "source",
            "requires_python": "~=3.6",
            "size": 46082,
            "upload_time": "2019-01-16T17:18:37",
            "url": "https://files.pythonhosted.org/packages/55/56/7f6b9dcb85c31c7e1775cc8fbb8703bcccf1df56d79629e23e1ff977b0b2/seqPresenceAbsence-0.2.2.tar.gz"
        }
    ]
}