{ "info": { "author": "Brant Faircloth", "author_email": "brant.faircloth+edittag@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 4 - Beta", "Environment :: Console", "Intended Audience :: Science/Research", "License :: OSI Approved :: BSD License", "Operating System :: OS Independent", "Programming Language :: Python", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "Copyright (c) 2009-2012 Brant C. Faircloth. All rights reserved.\n\n- See **LICENSE.md** for standard computer code.\n\n- Sequence tags available from\n https://github.com/faircloth-lab/edittag/downloads are licensed under\n `Creative Commons Attribution 3.0 United States License`_.\n\nDescription\n-----------\n\nedittag is a software collection for designing sets of edit metric\nsequence tags, checking sequence tags for conformation to the edit\nmetric, and integrating sequence tags to platform-specific sequencing\nadapters and PCR primers. edittag differs from other approaches:\n\n- edittag generates arbitrary lengths of edit-metric sequence tags in\n reasonable time frames using multiprocessing\n- edittag produces edit metric sequence tag sets conform to the edit\n distance selected\n- edittag used primer3 to integrate sequence tags to PCR primers\n\nWe provide several large sets of edit metric sequence tags designed\nusing edittag in the following formats:\n\n- text_ - this file is in an appropriate format for `check_levenshtien_distance.py`\n- csv_\n- `sqlite database`_\n\nDocumentation\n-------------\nYou can find documentation here:\n\nhttp://faircloth-lab.github.com/edittag/\n\nCitation\n--------\n\nFaircloth BC, Glenn TC. Large sets of edit-metric sequence identification \ntags to facilitate large-scale multiplexing of reads from massively \nparallel sequencing. `http://precedings.nature.com/documents/5672/version/1`_\n\nDependencies\n------------\n\n- `Python 2.7.x`_ (should work on 2.6.x)\n- `numpy`_ (tested with 1.5.1)\n- `py-levenshtein`_ [optional - strongly recommended]\n- `mod-primer3`_ [optional - needed for amplicon tagging]\n- `nose`_ [optional - for unittests]\n\nAvailability\n------------\n\n- tar.gz\n- repository\n\nInstallation\n------------\n\neasy_install\n~~~~~~~~~~~~\n::\n\n easy_install edittag\n\n\ntar.gz\n~~~~~~~\n::\n\n wget package.tar.gz\n tar -xzf package.tar.gz\n python setup.py install\n\n\nrepository\n~~~~~~~~~~~~\n::\n\n git clone git://github.com/faircloth-lab/edittag.git edittag\n\n\noptional package (py-levenshtein)\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n::\n\n wget http://pylevenshtein.googlecode.com/files/python-Levenshtein-0.10.1.tar.bz2\n tar -xzvf python-Levenshtein-0.10.1.tar.bz2\n python setup.py install\n\n\noptional package (primer3)\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nIf you wish to design primers incorporating edit metric sequence tags, you \nneed to first install a modified version of primer3:::\n\n git clone git://github.com/baddna/mod-primer3.git\n cd mod-primer3/src\n make\n\nEnsure that you move the binaries from mod-primer3 to a location in your\npath (move at least ``primer3-long`` and ``primer3_config`` into identical \ndirectories in your path).\n\nTesting\n--------\n\n::\n\n # Testing requires numpy and nose\n import edittag\n edittag.test()\n\n\nUsing edittag\n---------------\n\n::\n\n # generate some tags\n % design_edit_metric_tags.py --tag-length=6 --edit-distance=3 \\\n --no-polybase --gc --comp --min-and-greater --output tmp/tags.txt\n\n # validate the 6 nucleotide, edit distance 3 tag set\n % validate_edit_metric_tags.py \n --input=tmp/tags.txt\n --section='6nt ed3'\n --verbose\n\n # add those tags to a primer set\n % add_tags_to_primers.py --left-primer=GTTATGCATGAACGTAATGCTC \n --right-primer=CGCGCATGGTGGATTCACAATCC \\\n --input tmp/tags.txt --section='6nt ed3'\n --sort=pair_hairpin_either,pair_penalty,cycles \\\n --remove-common --keep-database \\\n --output tmp/trnH_tagged_with_10_nt_ed_5_tags.csv\n\n\n\n.. _`https://github.com/BadDNA/edittag/downloads`: https://github.com/BadDNA/edittag/downloads\n.. _`http://precedings.nature.com/documents/5672/version/1`: http://precedings.nature.com/documents/5672/version/1\n.. _Creative Commons Attribution 3.0 United States License: http://creativecommons.org/licenses/by/3.0/us/\n.. _text: https://github.com/downloads/faircloth-lab/edittag/edit_metric_tags.txt\n.. _csv: https://github.com/downloads/faircloth-lab/edittag/edit_metric_tags.csv\n.. _sqlite database: https://github.com/downloads/faircloth-lab/edittag/edit_metric_tags.sqlite.zip\n.. _Python 2.7.x: http://www.python.org/\n.. _numpy: http://numpy.scipy.org\n.. _py-levenshtein: http://pylevenshtein.googlecode.com\n.. _mod-primer3: https://github.com/BadDNA/mod-primer3\n.. _nose: http://somethingaboutorange.com/mrl/projects/nose/1.0.0/", "description_content_type": null, "docs_url": null, "download_url": "UNKNOWN", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "http://github.com/faircloth-lab/edittag/", "keywords": null, "license": "http://www.opensource.org/licenses/BSD-3-Clause", "maintainer": null, "maintainer_email": null, "name": "edittag", "package_url": "https://pypi.org/project/edittag/", "platform": "UNKNOWN", "project_url": "https://pypi.org/project/edittag/", "project_urls": { "Download": "UNKNOWN", "Homepage": "http://github.com/faircloth-lab/edittag/" }, "release_url": "https://pypi.org/project/edittag/1.1/", "requires_dist": null, "requires_python": null, "summary": "Design and check sets of edit metric sequence tags.", "version": "1.1" }, "last_serial": 791554, "releases": { "1.0": [ { "comment_text": "", "digests": { "md5": "1aaf6435b533a6ce3a35a72139a987f7", "sha256": "3dc128ed0d6ef0bac60c670feb74d316ad9b28d049128ee34bacdc3703c729f7" }, "downloads": -1, "filename": "edittag-1.0-py2.7.egg", "has_sig": false, "md5_digest": "1aaf6435b533a6ce3a35a72139a987f7", "packagetype": "bdist_egg", "python_version": "2.7", "requires_python": null, "size": 109545, "upload_time": "2011-05-07T04:17:06", "url": "https://files.pythonhosted.org/packages/77/a6/0fed623434eff06fe9737788567bc705a4f53424c1535134c0e9c3362f73/edittag-1.0-py2.7.egg" }, { "comment_text": "", "digests": { "md5": "2b64c58b8b7f76217fd00f14ba45030c", "sha256": "7d817c1867ea76f5b41d70d30d7c8e16a802d76361b0935c887b603539e4a88a" }, "downloads": -1, "filename": "edittag-1.0.tar.gz", "has_sig": false, "md5_digest": "2b64c58b8b7f76217fd00f14ba45030c", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 106801, "upload_time": "2011-05-07T04:16:38", "url": "https://files.pythonhosted.org/packages/05/51/8baefe780ca7cafec4de538eb88ec2af84fa228f61f0ba53180a613fc491/edittag-1.0.tar.gz" } ], "1.1": [ { "comment_text": "", "digests": { "md5": "b234881f573049c89ee16d8bdff5413f", "sha256": "8d4b06efa50dc71ceae69958bfc080c53de4bf20de53a3cb07e3a0b6da2a14ab" }, "downloads": -1, "filename": "edittag-1.1.tar.gz", "has_sig": false, "md5_digest": "b234881f573049c89ee16d8bdff5413f", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 108071, "upload_time": "2012-07-13T07:50:00", "url": "https://files.pythonhosted.org/packages/4d/9d/1545494f40586784d3801fc2f223c2a55d5a7fd32fc36b08a6ffc30d249f/edittag-1.1.tar.gz" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "b234881f573049c89ee16d8bdff5413f", "sha256": "8d4b06efa50dc71ceae69958bfc080c53de4bf20de53a3cb07e3a0b6da2a14ab" }, "downloads": -1, "filename": "edittag-1.1.tar.gz", "has_sig": false, "md5_digest": "b234881f573049c89ee16d8bdff5413f", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 108071, "upload_time": "2012-07-13T07:50:00", "url": "https://files.pythonhosted.org/packages/4d/9d/1545494f40586784d3801fc2f223c2a55d5a7fd32fc36b08a6ffc30d249f/edittag-1.1.tar.gz" } ] }