{ "info": { "author": "Tim Stuart", "author_email": "tstuart@nygenome.org", "bugtrack_url": null, "classifiers": [ "Intended Audience :: Science/Research", "License :: OSI Approved :: MIT License", "Operating System :: OS Independent", "Programming Language :: Python :: 3" ], "description": "# sinto\nTools for single-cell data processing\n\n## Installation\n\nInstall from PyPI:\n\n```bash\npip install sinto\n```\n\nInstall from source:\n\n```bash\ngit clone https://github.com/timoast/sinto.git\ncd sinto\npython setup.py install\n```\n\n## Features\n\n### Filter barcodes\n\nSubsets of cells can be extracted from a BAM file using the \n`sinto filterbarcodes` command:\n\n```\n$ sinto filterbarcodes -h\nusage: sinto filterbarcodes [-h] -b BAM -c CELLS -o OUTPUT [-t] [-s]\n [-p NPROC] [-m MODE]\n\nFilter reads based on input list of cell barcodes\n\noptional arguments:\n -h, --help show this help message and exit\n -b BAM, --bam BAM Input bam file (must be indexed)\n -c CELLS, --cells CELLS\n File or comma-separated list of cell barcodes. Can be\n gzip compressed\n -o OUTPUT, --output OUTPUT\n Name for output text file\n -t, --trim_suffix Remove trail 2 characters from cell barcode in BAM\n file\n -s, --sam Output sam format (default bam output)\n -p NPROC, --nproc NPROC\n Number of processors (default = 1)\n -m MODE, --mode MODE Either tag (default) or readname. Some BAM file store\n the cell barcode in the readname rather than under a\n read tag\n```\n\n### Add read tags per cell\n\nDifferent read tags can be added to each cell with \nthe `sinto addtags` command. \n\n```\n$ sinto addtags -h\nusage: sinto addtags [-h] -b BAM -f TAGFILE -o OUTPUT [-t] [-s] [-p NPROC]\n [-m MODE]\n\nAdd read tags to reads from individual cells\n\noptional arguments:\n -h, --help show this help message and exit\n -b BAM, --bam BAM Input bam file (must be indexed)\n -f TAGFILE, --tagfile TAGFILE\n Tab-delimited file containing cell barcode, tag to be\n added, and tag identity. Can be gzip compressed\n -o OUTPUT, --output OUTPUT\n Name for output text file\n -t, --trim_suffix Remove trail 2 characters from cell barcode in BAM\n file\n -s, --sam Output sam format (default bam output)\n -p NPROC, --nproc NPROC\n Number of processors (default = 1)\n -m MODE, --mode MODE Either tag (default) or readname. Some BAM file store\n the cell barcode in the readname rather than under a\n read tag\n```\n\nThis requires a file specifying the tags to be added to each cell, for example:\n\n```\nTGGCAATGTTGAAGCG-1\tCI\tA\nGACCAATCACCATTCC-1\tCI\tA\nCAGGATTCAGAACTTC-1\tCI\tB\nGAACCTAAGAGAGGTA-1\tCI\tB\nACATGGTGTAGACGCA-1\tCI\tC\nCCCTGATTCGGATAGG-1\tCI\tC\n```\n\nThis will add a `CI` tag, with the tag set to A, B, or C depending on the cell barcode sequence.\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/timoast/sinto", "keywords": "", "license": "", "maintainer": "", "maintainer_email": "", "name": "sinto", "package_url": "https://pypi.org/project/sinto/", "platform": "", "project_url": "https://pypi.org/project/sinto/", "project_urls": { "Homepage": "https://github.com/timoast/sinto" }, "release_url": "https://pypi.org/project/sinto/0.2/", "requires_dist": [ "pysam (>=0.8)" ], "requires_python": "", "summary": "sinto: tools for single-cell data processing", "version": "0.2" }, "last_serial": 5130748, "releases": { "0.1": [ { "comment_text": "", "digests": { "md5": "62a5a8ccb0508b115623967421661f6a", "sha256": "9bc7a23c9f3ceab92cb59803195dec113d8d80b976e62aa8a55c51d9136c9868" }, "downloads": -1, "filename": "sinto-0.1-py3-none-any.whl", "has_sig": false, "md5_digest": "62a5a8ccb0508b115623967421661f6a", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": null, "size": 5967, "upload_time": "2019-04-01T18:34:55", "url": "https://files.pythonhosted.org/packages/b0/75/3fa7276854c9067fd6bc777edf31f218e8119d3a16102b7497b0be1dfecc/sinto-0.1-py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "e13b7e62296543fb6e8aa7b56ad27725", "sha256": "81f41607a2592e5cd9f30d6930b1ac38b9884d2eaf5253e3f6a788c23e83686d" }, "downloads": -1, "filename": "sinto-0.1.tar.gz", "has_sig": false, "md5_digest": "e13b7e62296543fb6e8aa7b56ad27725", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 20625, "upload_time": "2019-04-01T18:34:57", "url": "https://files.pythonhosted.org/packages/d6/04/eef3525fbfd4c1c1a777f97615260d9f992be6d24a78c9fd58d24a286e3a/sinto-0.1.tar.gz" } ], "0.2": [ { "comment_text": "", "digests": { "md5": "93d3cecd9f8d46a4b9457053da46a327", "sha256": "3aac5f55a8367b3eda43bfad61498169a0db344e4da1f3b86e3eafb8fedcdca8" }, "downloads": -1, "filename": "sinto-0.2-py3-none-any.whl", "has_sig": false, "md5_digest": "93d3cecd9f8d46a4b9457053da46a327", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": null, "size": 8235, "upload_time": "2019-04-11T19:58:09", "url": "https://files.pythonhosted.org/packages/bb/61/30b7c3476fe7cb1c185425d49810d52ca27d7f8d77feefb6f370adf5d0a2/sinto-0.2-py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "06a364204c7695b02440c9ef70a7aa91", "sha256": "93ba21d4e2c09927b8c0e2ea8992597a297408fa6b773fdb1de3acddef126d9f" }, "downloads": -1, "filename": "sinto-0.2.tar.gz", "has_sig": false, "md5_digest": "06a364204c7695b02440c9ef70a7aa91", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 21686, "upload_time": "2019-04-11T19:58:10", "url": "https://files.pythonhosted.org/packages/3e/d1/5ce78cc1c31c290830a55f507a04b9ea25582a4024651477fd51bf73cfaa/sinto-0.2.tar.gz" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "93d3cecd9f8d46a4b9457053da46a327", "sha256": "3aac5f55a8367b3eda43bfad61498169a0db344e4da1f3b86e3eafb8fedcdca8" }, "downloads": -1, "filename": "sinto-0.2-py3-none-any.whl", "has_sig": false, "md5_digest": "93d3cecd9f8d46a4b9457053da46a327", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": null, "size": 8235, "upload_time": "2019-04-11T19:58:09", "url": "https://files.pythonhosted.org/packages/bb/61/30b7c3476fe7cb1c185425d49810d52ca27d7f8d77feefb6f370adf5d0a2/sinto-0.2-py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "06a364204c7695b02440c9ef70a7aa91", "sha256": "93ba21d4e2c09927b8c0e2ea8992597a297408fa6b773fdb1de3acddef126d9f" }, "downloads": -1, "filename": "sinto-0.2.tar.gz", "has_sig": false, "md5_digest": "06a364204c7695b02440c9ef70a7aa91", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 21686, "upload_time": "2019-04-11T19:58:10", "url": "https://files.pythonhosted.org/packages/3e/d1/5ce78cc1c31c290830a55f507a04b9ea25582a4024651477fd51bf73cfaa/sinto-0.2.tar.gz" } ] }