{ "info": { "author": "Lenz Furrer", "author_email": "furrer@cl.uzh.ch", "bugtrack_url": null, "classifiers": [ "License :: OSI Approved :: BSD License", "Operating System :: OS Independent", "Programming Language :: Python :: 3" ], "description": "# TAP-k -- Python module for Threshold Average Precision\n\nThreshold Average Precision is a metric for evaluating IR applications that present retrieval lists with a ranking score to the end user.\nIt is described in the following publication:\n\n> Hyrum D. Carroll, Maricel G. Kann, Sergey L. Sheetlin, and John L. Spouge: \"Threshold Average Precision (TAP-_k_): A Measure of Retrieval Efficacy Designed for Bioinformatics\" (2010). Bioinformatics 26(14):1708-1713. DOI: 10.1093/bioinformatics/btq270\n\nThis Python module is based on the authors' reference implementation written in Perl, which can be found at http://www.ncbi.nlm.nih.gov/CBBresearch/Spouge/html.ncbi/tap/.\n\n\n## Installation\n\nUse `pip` for a system-wide installation:\n\n pip3 install TAP-k\n\nOr simply download the stand-alone script [tapk.py](https://github.com/OntoGene/TAP-k/blob/master/tapk.py).\n\n\n## Requirements\n\n`TAP-k` runs on Python 3 (Python 3.4 or higher recommended). \nNo other requirements.\n\n\n## Usage\n\nInstalling via `pip` creates an executable script *TAP-k* to run from the command line:\n\n TAP-k [options]\n\nIf you just downloaded the stand-alone module, use the following call:\n\n python3 tapk.py [options]\n\nRun `TAP-k --help` to see a short description of all available options.\n\nExample call with minimal output:\n\n $ TAP-k -i test/short.tsv -k 5 -s\n EPQ (threshold at 0.5 quantile)\tunweighted mean TAP\n 5 (0.6545522081334377)\t0.5664\n\nThe input file format is the same as for the original program, which is described [here](https://www.ncbi.nlm.nih.gov/CBBresearch/Spouge/html_ncbi/html/tap/help.html).\nAll output is written to STDOUT.\nThe output format can be changed by specifying format strings (options `-f` and `-Q`).\n\nThe module can also be used as a library:\n\n```pycon\n>>> import tapk\n>>> retlists = ['test/retlists/{}.tsv'.format(fn)\n for fn in ('weighted', 'single')]\n>>> result = tapk.tapk(retlists, k=5)\n>>> result.tap\n0.1311308349769888\n>>> result.e0\n0.7418847867396157\n>>> result.queries\n[QueryResult(query='23817572', tap=0.22749287749287747, weight=3.0, T_q=8),\n QueryResult(query='12954810', tap=0.0, weight=1.0, T_q=1),\n QueryResult(query='20729916', tap=0.08055555555555555, weight=2.0, T_q=1),\n QueryResult(query='21519793', tap=0.0, weight=5.0, T_q=1),\n QueryResult(query='7787496', tap=0.5833333333333334, weight=1.0, T_q=1),\n QueryResult(query='1303262', tap=0.27777777777777773, weight=1.0, T_q=2)]\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/OntoGene/TAP-k", "keywords": "", "license": "", "maintainer": "", "maintainer_email": "", "name": "TAP-k", "package_url": "https://pypi.org/project/TAP-k/", "platform": "", "project_url": "https://pypi.org/project/TAP-k/", "project_urls": { "Homepage": "https://github.com/OntoGene/TAP-k" }, "release_url": "https://pypi.org/project/TAP-k/1.0/", "requires_dist": null, "requires_python": ">=3", "summary": "Threshold Average Precision: metric for evaluating retrieval rankings", "version": "1.0" }, "last_serial": 4577874, "releases": { "1.0": [ { "comment_text": "", "digests": { "md5": "df4e32c71f87966dc70281f5fac85f7c", "sha256": "de1c2c07cae06aa5b6cb638ba61fd8f21db2a14f6796b6fb840bd723ba1f3ba6" }, "downloads": -1, "filename": "TAP_k-1.0-py3-none-any.whl", "has_sig": false, "md5_digest": "df4e32c71f87966dc70281f5fac85f7c", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": ">=3", "size": 10230, "upload_time": "2018-12-09T18:41:03", "url": "https://files.pythonhosted.org/packages/27/40/cc6b4f00b127785bf30af8ab225db9e9f7c826b4ab2f80156355d6fa6962/TAP_k-1.0-py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "06a5b7ba29fd26490132008dbba86280", "sha256": "f688606dc42e9623acc1fd30e232529ee564c6cdd368d88281944c39594f1927" }, "downloads": -1, "filename": "TAP-k-1.0.tar.gz", "has_sig": false, "md5_digest": "06a5b7ba29fd26490132008dbba86280", "packagetype": "sdist", "python_version": "source", "requires_python": ">=3", "size": 9632, "upload_time": "2018-12-09T18:41:05", "url": "https://files.pythonhosted.org/packages/aa/0e/7cce98081806b9c32bf766ad4a0b8acffe67bfac56c88632ceed2e5b4050/TAP-k-1.0.tar.gz" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "df4e32c71f87966dc70281f5fac85f7c", "sha256": "de1c2c07cae06aa5b6cb638ba61fd8f21db2a14f6796b6fb840bd723ba1f3ba6" }, "downloads": -1, "filename": "TAP_k-1.0-py3-none-any.whl", "has_sig": false, "md5_digest": "df4e32c71f87966dc70281f5fac85f7c", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": ">=3", "size": 10230, "upload_time": "2018-12-09T18:41:03", "url": "https://files.pythonhosted.org/packages/27/40/cc6b4f00b127785bf30af8ab225db9e9f7c826b4ab2f80156355d6fa6962/TAP_k-1.0-py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "06a5b7ba29fd26490132008dbba86280", "sha256": "f688606dc42e9623acc1fd30e232529ee564c6cdd368d88281944c39594f1927" }, "downloads": -1, "filename": "TAP-k-1.0.tar.gz", "has_sig": false, "md5_digest": "06a5b7ba29fd26490132008dbba86280", "packagetype": "sdist", "python_version": "source", "requires_python": ">=3", "size": 9632, "upload_time": "2018-12-09T18:41:05", "url": "https://files.pythonhosted.org/packages/aa/0e/7cce98081806b9c32bf766ad4a0b8acffe67bfac56c88632ceed2e5b4050/TAP-k-1.0.tar.gz" } ] }