{
    "info": {
        "author": "David Seifert, Susana Posada Cespedes",
        "author_email": "david.seifert@bsse.ethz.ch, susana.posada@bsse.ethz.ch",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 3 - Alpha",
            "License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.4",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
            "Topic :: Utilities"
        ],
        "description": "####################\nsmallgenomeutilities\n####################\n\nThe smallgenomeutilities are a collection of scripts that is useful for dealing and manipulating NGS data of small viral genomes. They are written in Python 3 with a small number of dependencies.\n\n\n************\nDependencies\n************\n\n- biopython\n- numpy\n- progress\n- pysam\n- sklearn\n- matplotlib\n\n************\nInstallation\n************\n\nThe recommended way to install the smallgenomeutilities is using pip:\n\n.. code-block:: bash\n\n   pip install smallgenomeutilities\n\n\n************************\nDescription of utilities\n************************\n\ncompute_mds\n___________\nCompute multidimensional scaling for visualizing distances among reconstructed haplotypes.\n\nconvert_qr\n----------\nConvert QuasiRecomb output of a transmitter and recipient set of haplotypes to a combined set of haplotypes, where gaps have been filtered. Optionally translate to peptide sequence.\n\nconvert_reference\n-----------------\nPerform a genomic liftover. Transform an alignment in SAM or BAM format from one reference sequence to another. Can replace `M` states by `=`/`X`.\n\ncoverage\n--------\nCalculate average coverage for a target region on a different contig.\n\ncoverage_stats\n--------------\nCalculate average coverage for a target region of an alignment.\n\nextract_coverage_intervals\n--------------------------\nExtract regions with sufficient coverage for running ShoRAH. Half-open intervals are returned, [start:end), and 0-based indexing is used.\n\nextract_sam\n-----------\nExtract subsequences of an alignment, with the option of converting it to peptide sequences. Can filter on the basis of subsequence frequency or gap frequencies in subsequences.\n\nextract_seq\n-----------\nExtract sequences of alignments into a FASTA file where the sequence id matches a given string.\n\nmapper\n------\nDetermine the genomic offsets on a target contig, given an initial contig and offsets. Can be used to map between reference genomes.\n\nminority_freq\n-------------\nExtract frequencies of minority variants from multiple samples. A region of interest is also supported.\n\npair_sequences\n--------------\nCompare sequences from a multiple sequence alignment from transmitter and recipient samples in order to determine the optimal matching of transmitters to recipients.\n\npredict_num_reads\n-----------------\nPredict number of reads after quality preprocessing. \n\nremove_gaps_msa\n---------------\nGiven a multiple sequence alignment, remove loci with a gap fraction above a certain threshold.\n\n\n*************\nContributions\n*************\n\n- David Seifert <david.seifert@bsse.ethz.ch>\n- Susana Posada Cespedes <susana.posada@bsse.ethz.ch>\n",
        "description_content_type": null,
        "docs_url": null,
        "download_url": "",
        "downloads": {
            "last_day": -1,
            "last_month": -1,
            "last_week": -1
        },
        "home_page": "https://github.com/cbg-ethz/smallgenomeutilities",
        "keywords": "NGS SAM BAM HIV-1 alignment",
        "license": "GPL2+",
        "maintainer": "",
        "maintainer_email": "",
        "name": "smallgenomeutilities",
        "package_url": "https://pypi.org/project/smallgenomeutilities/",
        "platform": "",
        "project_url": "https://pypi.org/project/smallgenomeutilities/",
        "project_urls": {
            "Homepage": "https://github.com/cbg-ethz/smallgenomeutilities"
        },
        "release_url": "https://pypi.org/project/smallgenomeutilities/0.2.1/",
        "requires_dist": null,
        "requires_python": "",
        "summary": "A collection of scripts that are useful for dealing with viral RNA NGS data.",
        "version": "0.2.1"
    },
    "last_serial": 3328428,
    "releases": {
        "0.1": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "339439b1f97ecb1fc91378f78a06bebe",
                    "sha256": "8d9ee58ba2748e85c27c18feaa3f7c1e71b04c40bd46bdf846ea604ff8b5789e"
                },
                "downloads": -1,
                "filename": "smallgenomeutilities-0.1.tar.gz",
                "has_sig": false,
                "md5_digest": "339439b1f97ecb1fc91378f78a06bebe",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 22799,
                "upload_time": "2017-06-02T12:44:38",
                "url": "https://files.pythonhosted.org/packages/16/30/b2b629f57a7e1d88c1be86ff30314988b458d70eda0d0c46ea91aa470e77/smallgenomeutilities-0.1.tar.gz"
            }
        ],
        "0.2": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "041a743d17ae68d4503c8fb50ae8fa4b",
                    "sha256": "e1c515f237e091c09aa74a37ad3b8bbf6c04be35a9a8fac541da2617d7c07307"
                },
                "downloads": -1,
                "filename": "smallgenomeutilities-0.2-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "041a743d17ae68d4503c8fb50ae8fa4b",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": null,
                "size": 36843,
                "upload_time": "2017-11-09T16:49:28",
                "url": "https://files.pythonhosted.org/packages/a7/a9/64e76ab93a7eeb8be7dcbd89d445685b4809d33d0dcc79226de401b6705e/smallgenomeutilities-0.2-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "f8b222892e9f18bb135efd5802a878a4",
                    "sha256": "802ca5f85a14e8243aa44e5f4fb771691f0c80689cf3ecb1edce5382ce0ecda3"
                },
                "downloads": -1,
                "filename": "smallgenomeutilities-0.2.tar.gz",
                "has_sig": false,
                "md5_digest": "f8b222892e9f18bb135efd5802a878a4",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 26888,
                "upload_time": "2017-11-09T16:49:29",
                "url": "https://files.pythonhosted.org/packages/f8/e2/54b075294a3247595abf9f7d7314eddc04c77a049398157514b65087fe6a/smallgenomeutilities-0.2.tar.gz"
            }
        ],
        "0.2.1": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "ef7b67720f5627910c55039cebd0b214",
                    "sha256": "3268f0074ae0d03478f3bab89461209c099243f81816afc80cfd3ebe7eb261e1"
                },
                "downloads": -1,
                "filename": "smallgenomeutilities-0.2.1-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "ef7b67720f5627910c55039cebd0b214",
                "packagetype": "bdist_wheel",
                "python_version": "3.6",
                "requires_python": null,
                "size": 38784,
                "upload_time": "2017-11-13T12:48:10",
                "url": "https://files.pythonhosted.org/packages/46/20/dc6806fb9ee6714c06aa3e65149e840d562567b3d9ed66dc5fdfea471ab4/smallgenomeutilities-0.2.1-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "ad135513329f90d116a71177b7c567b6",
                    "sha256": "81bf3c83169b1fe3304f32a73773ddf559bbde7adda59c1a5a3d816cb746b138"
                },
                "downloads": -1,
                "filename": "smallgenomeutilities-0.2.1.tar.gz",
                "has_sig": false,
                "md5_digest": "ad135513329f90d116a71177b7c567b6",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 33739,
                "upload_time": "2017-11-13T12:39:24",
                "url": "https://files.pythonhosted.org/packages/a3/9c/4b90373c6347be8f70d9c582f40d2709ce87ab038fb7cf89e4c3472380e0/smallgenomeutilities-0.2.1.tar.gz"
            }
        ]
    },
    "urls": [
        {
            "comment_text": "",
            "digests": {
                "md5": "ef7b67720f5627910c55039cebd0b214",
                "sha256": "3268f0074ae0d03478f3bab89461209c099243f81816afc80cfd3ebe7eb261e1"
            },
            "downloads": -1,
            "filename": "smallgenomeutilities-0.2.1-py3-none-any.whl",
            "has_sig": false,
            "md5_digest": "ef7b67720f5627910c55039cebd0b214",
            "packagetype": "bdist_wheel",
            "python_version": "3.6",
            "requires_python": null,
            "size": 38784,
            "upload_time": "2017-11-13T12:48:10",
            "url": "https://files.pythonhosted.org/packages/46/20/dc6806fb9ee6714c06aa3e65149e840d562567b3d9ed66dc5fdfea471ab4/smallgenomeutilities-0.2.1-py3-none-any.whl"
        },
        {
            "comment_text": "",
            "digests": {
                "md5": "ad135513329f90d116a71177b7c567b6",
                "sha256": "81bf3c83169b1fe3304f32a73773ddf559bbde7adda59c1a5a3d816cb746b138"
            },
            "downloads": -1,
            "filename": "smallgenomeutilities-0.2.1.tar.gz",
            "has_sig": false,
            "md5_digest": "ad135513329f90d116a71177b7c567b6",
            "packagetype": "sdist",
            "python_version": "source",
            "requires_python": null,
            "size": 33739,
            "upload_time": "2017-11-13T12:39:24",
            "url": "https://files.pythonhosted.org/packages/a3/9c/4b90373c6347be8f70d9c582f40d2709ce87ab038fb7cf89e4c3472380e0/smallgenomeutilities-0.2.1.tar.gz"
        }
    ]
}