{
    "info": {
        "author": "Gerry Tonkin-Hill",
        "author_email": "g.tonkinhill@gmail.com",
        "bugtrack_url": null,
        "classifiers": [
            "License :: OSI Approved :: MIT License",
            "Operating System :: OS Independent",
            "Programming Language :: Python :: 3.6"
        ],
        "description": "# pairsnp-python\n\n[![Travis-CI Build Status](https://travis-ci.com/gtonkinhill/pairsnp-python.svg?branch=master)](https://travis-ci.com/gtonkinhill/pairsnp-python)\n\n## Installation\n\nThis is a Python3 version of pairsnp written with the help of Simon Frost\n\n```\ngit clone https://github.com/gtonkinhill/pairsnp-python\ncd pairsnp-python\npip3 install .\n```\n\n## Quick Start\n\nThe python version can be run from the python interpreter as\n\n```\nfrom pairsnp import calculate_snp_matrix, calculate_distance_matrix\n\nsparse_matrix, consensus, seq_names = calculate_snp_matrix(fasta.file.name)\nd = calculate_distance_matrix(sparse_matrix, consensus, \"dist\", False)\n```\n\nalternatively if installed using pip it can be used at the command line as\n\n\n```\npairsnp -f /path/to/msa.fasta -o /path/to/output.csv\n```\n\nadditional options include\n\n```\nProgram to calculate pairwise SNP distance and similarity matrices.\n\noptional arguments:\n  -h, --help            show this help message and exit\n  -t {sim,dist}, --type {sim,dist}\n                        either sim (similarity) or dist (distance) (default).\n  -n, --inc_n           flag to indicate differences to gaps should be\n                        counted.\n  -f FILENAME, --file FILENAME\n                        location of a multiple sequence alignment. Currently\n                        only DNA alignments are supported.\n  -z, --zipped          Alignment is gzipped.\n  -c, --csv             Output csv-delimited table (default tsv).\n  -o OUTPUT, --out OUTPUT\n                        location of output file.\n```\n\n\n",
        "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/gtonkinhill/pairsnp/",
        "keywords": "",
        "license": "",
        "maintainer": "",
        "maintainer_email": "",
        "name": "pairsnp",
        "package_url": "https://pypi.org/project/pairsnp/",
        "platform": "",
        "project_url": "https://pypi.org/project/pairsnp/",
        "project_urls": {
            "Homepage": "https://github.com/gtonkinhill/pairsnp/"
        },
        "release_url": "https://pypi.org/project/pairsnp/0.0.7/",
        "requires_dist": [
            "numpy",
            "scipy"
        ],
        "requires_python": "",
        "summary": "A simple package for calculating pairwise SNP distances",
        "version": "0.0.7"
    },
    "last_serial": 5081259,
    "releases": {
        "0.0.3": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "aed01fb2fe6b9cb285bd35dbe892ee05",
                    "sha256": "f06711ff8ce9548f25bb6e58ddec01a3b8bda6b6896b460acc27dc227319f891"
                },
                "downloads": -1,
                "filename": "pairsnp-0.0.3-py2.7.egg",
                "has_sig": false,
                "md5_digest": "aed01fb2fe6b9cb285bd35dbe892ee05",
                "packagetype": "bdist_egg",
                "python_version": "2.7",
                "requires_python": null,
                "size": 6393,
                "upload_time": "2018-09-28T15:01:00",
                "url": "https://files.pythonhosted.org/packages/55/95/f3c727c5303f46f6e5e83a0b6a0f2677d174f48f8781abc429934a660a94/pairsnp-0.0.3-py2.7.egg"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "b8136eb5aba043b009bcbff1ca7b3d8e",
                    "sha256": "1d78c784111dc7382e1958392c160063663a17d4cf63df397dcc1c8b63c9ec46"
                },
                "downloads": -1,
                "filename": "pairsnp-0.0.3-py2-none-any.whl",
                "has_sig": false,
                "md5_digest": "b8136eb5aba043b009bcbff1ca7b3d8e",
                "packagetype": "bdist_wheel",
                "python_version": "py2",
                "requires_python": null,
                "size": 4504,
                "upload_time": "2018-08-22T15:07:26",
                "url": "https://files.pythonhosted.org/packages/a0/ba/5e858e3af820436af7367d179baa63ad3441206762d7a9cacfbbbc8b490b/pairsnp-0.0.3-py2-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "f1e23546936e382811d2145073bee8c6",
                    "sha256": "e6d72845b4b74248f720f9d6b17f47aa8c532f19bf039df0aba67f3ff966143f"
                },
                "downloads": -1,
                "filename": "pairsnp-0.0.3.tar.gz",
                "has_sig": false,
                "md5_digest": "f1e23546936e382811d2145073bee8c6",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 2972,
                "upload_time": "2018-08-22T15:07:27",
                "url": "https://files.pythonhosted.org/packages/05/e6/dc7ac5059e237d2316d1bf0678b1734fbe6310c71a4df4da09aab6142c87/pairsnp-0.0.3.tar.gz"
            }
        ],
        "0.0.4": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "0f4c47eba9b1e7b9242d3e7a974f3dbf",
                    "sha256": "0137523110d8d2209a956b1c82d25d5aa9bc42dc8a4eb4ccda716b9707ac60a4"
                },
                "downloads": -1,
                "filename": "pairsnp-0.0.4-py2.7.egg",
                "has_sig": false,
                "md5_digest": "0f4c47eba9b1e7b9242d3e7a974f3dbf",
                "packagetype": "bdist_egg",
                "python_version": "2.7",
                "requires_python": null,
                "size": 7724,
                "upload_time": "2018-09-28T15:01:02",
                "url": "https://files.pythonhosted.org/packages/54/28/acea3f6ef256055fc8df6c39a1e20c5da366a6d24e23a1cdc6a183774145/pairsnp-0.0.4-py2.7.egg"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "2bf0a245013b4291f161e60d5ed2b947",
                    "sha256": "fd8817d3f4c73301864b25661af407122c81c77d1622211fe07918c3e0b84e8f"
                },
                "downloads": -1,
                "filename": "pairsnp-0.0.4-py2-none-any.whl",
                "has_sig": false,
                "md5_digest": "2bf0a245013b4291f161e60d5ed2b947",
                "packagetype": "bdist_wheel",
                "python_version": "py2",
                "requires_python": null,
                "size": 5201,
                "upload_time": "2018-09-28T15:00:57",
                "url": "https://files.pythonhosted.org/packages/90/93/8be7d4c2f43fa2ba6975117e04b8f702111e12349ee35d9d37399d0e4c8a/pairsnp-0.0.4-py2-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "8138ab00b662600c662e3c2f668e73c7",
                    "sha256": "e5460ae54792d6d68b3139f48cb622bd5ff713a316d244f34fad09689c1409be"
                },
                "downloads": -1,
                "filename": "pairsnp-0.0.4.tar.gz",
                "has_sig": false,
                "md5_digest": "8138ab00b662600c662e3c2f668e73c7",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 3270,
                "upload_time": "2018-09-28T15:01:03",
                "url": "https://files.pythonhosted.org/packages/3c/9d/f7c8086091e8a3916243bf45be6810db18085b8c3ed2c85ca3073d7e2cba/pairsnp-0.0.4.tar.gz"
            }
        ],
        "0.0.5": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "07c84b8aab4a7927ea5e927617277f60",
                    "sha256": "fb995f058df85fecce0acc4d16060d4103dbc851828ec0d4b6fce9ffd32f0263"
                },
                "downloads": -1,
                "filename": "pairsnp-0.0.5-py2-none-any.whl",
                "has_sig": false,
                "md5_digest": "07c84b8aab4a7927ea5e927617277f60",
                "packagetype": "bdist_wheel",
                "python_version": "py2",
                "requires_python": null,
                "size": 5201,
                "upload_time": "2018-09-28T15:00:58",
                "url": "https://files.pythonhosted.org/packages/a7/0a/f8c2866b49443b7c6c51c671bae8d2e6aaf78441ebaa53fa0c2eaec261d7/pairsnp-0.0.5-py2-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "24ea4af81bfce9b2e5908ea89a5d83d3",
                    "sha256": "7373694d5c896aab22421664e72569f0514fce255a40a67b3548723011ade80d"
                },
                "downloads": -1,
                "filename": "pairsnp-0.0.5.tar.gz",
                "has_sig": false,
                "md5_digest": "24ea4af81bfce9b2e5908ea89a5d83d3",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 3271,
                "upload_time": "2018-09-28T15:01:04",
                "url": "https://files.pythonhosted.org/packages/fb/ed/7dad8b1a4da79f7dadd1c2862ffa02a33d570fd66e794becab18cd42d099/pairsnp-0.0.5.tar.gz"
            }
        ],
        "0.0.6": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "f3542b5bb8573a9d2a8d69789427d684",
                    "sha256": "9d29b63c6bc97f248055dfccc052120b215ddf979ee50d7cbb5f353cd1c8ac23"
                },
                "downloads": -1,
                "filename": "pairsnp-0.0.6-py2-none-any.whl",
                "has_sig": false,
                "md5_digest": "f3542b5bb8573a9d2a8d69789427d684",
                "packagetype": "bdist_wheel",
                "python_version": "py2",
                "requires_python": null,
                "size": 6595,
                "upload_time": "2018-10-05T10:50:11",
                "url": "https://files.pythonhosted.org/packages/cc/51/922036852c6676c478e994599046390199ae2ec4a7c0d15a01ae722c2b54/pairsnp-0.0.6-py2-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "3e9e1b597c7db873cb63e3bb6b5eed94",
                    "sha256": "c6fd55ef4268630015163e62b3c1c5f831f673c3f4b0acab8e600e7255c0a8d1"
                },
                "downloads": -1,
                "filename": "pairsnp-0.0.6.tar.gz",
                "has_sig": false,
                "md5_digest": "3e9e1b597c7db873cb63e3bb6b5eed94",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 3918,
                "upload_time": "2018-10-05T10:50:15",
                "url": "https://files.pythonhosted.org/packages/17/ca/319df1efc32a0388e744f36d91bd641e2435eaf13858a603d061780642cc/pairsnp-0.0.6.tar.gz"
            }
        ],
        "0.0.7": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "cd1fb41b57cd8e6829cba32f174923db",
                    "sha256": "35b68ed41de00589ada073fe87799c521d2b1e14f48423b7dbf098095e6c4e9b"
                },
                "downloads": -1,
                "filename": "pairsnp-0.0.7-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "cd1fb41b57cd8e6829cba32f174923db",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": null,
                "size": 5058,
                "upload_time": "2019-04-02T22:13:00",
                "url": "https://files.pythonhosted.org/packages/ba/a0/857046b4e157d86a542258f24062532c7ec27a0f092e4a4e46128394b47f/pairsnp-0.0.7-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "7f6b26ed596195fc9ce82ce1271929da",
                    "sha256": "591f395c59d91056882f0b349c201b2d708a093d6b6ffd3c2ee34aed8767ee98"
                },
                "downloads": -1,
                "filename": "pairsnp-0.0.7.tar.gz",
                "has_sig": false,
                "md5_digest": "7f6b26ed596195fc9ce82ce1271929da",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 3953,
                "upload_time": "2019-04-02T22:13:05",
                "url": "https://files.pythonhosted.org/packages/1b/f1/d229d96eff9acb851514f0bd9fb808fb0c36cf505f6896f8937f88b164e2/pairsnp-0.0.7.tar.gz"
            }
        ]
    },
    "urls": [
        {
            "comment_text": "",
            "digests": {
                "md5": "cd1fb41b57cd8e6829cba32f174923db",
                "sha256": "35b68ed41de00589ada073fe87799c521d2b1e14f48423b7dbf098095e6c4e9b"
            },
            "downloads": -1,
            "filename": "pairsnp-0.0.7-py3-none-any.whl",
            "has_sig": false,
            "md5_digest": "cd1fb41b57cd8e6829cba32f174923db",
            "packagetype": "bdist_wheel",
            "python_version": "py3",
            "requires_python": null,
            "size": 5058,
            "upload_time": "2019-04-02T22:13:00",
            "url": "https://files.pythonhosted.org/packages/ba/a0/857046b4e157d86a542258f24062532c7ec27a0f092e4a4e46128394b47f/pairsnp-0.0.7-py3-none-any.whl"
        },
        {
            "comment_text": "",
            "digests": {
                "md5": "7f6b26ed596195fc9ce82ce1271929da",
                "sha256": "591f395c59d91056882f0b349c201b2d708a093d6b6ffd3c2ee34aed8767ee98"
            },
            "downloads": -1,
            "filename": "pairsnp-0.0.7.tar.gz",
            "has_sig": false,
            "md5_digest": "7f6b26ed596195fc9ce82ce1271929da",
            "packagetype": "sdist",
            "python_version": "source",
            "requires_python": null,
            "size": 3953,
            "upload_time": "2019-04-02T22:13:05",
            "url": "https://files.pythonhosted.org/packages/1b/f1/d229d96eff9acb851514f0bd9fb808fb0c36cf505f6896f8937f88b164e2/pairsnp-0.0.7.tar.gz"
        }
    ]
}