{ "info": { "author": "Adam R. Rivers, Qingpeng Zhang", "author_email": "adam.rivers@ars.usda.gov", "bugtrack_url": null, "classifiers": [ "Development Status :: 3 - Alpha", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6", "Topic :: Scientific/Engineering :: Artificial Intelligence", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "Vica: Software to identify highly divergent DNA and RNA viruses and phages in microbiomes\n=========================================================================================\n.. image:: https://travis-ci.org/USDA-ARS-GBRU/vica.svg?branch=master\n :target: https://travis-ci.org/USDA-ARS-GBRU/vica\n\n.. image:: https://codecov.io/gh/USDA-ARS-GBRU/vica/branch/master/graph/badge.svg\n :target: https://codecov.io/gh/USDA-ARS-GBRU/vica\n\n.. image:: https://readthedocs.org/projects/vica/badge/?version=latest\n :target: http://vica.readthedocs.io/en/latest/?badge=latest\n :alt: Documentation Status\n\n.. image:: https://api.codacy.com/project/badge/Grade/f39e8359ea334739842bba35e596cfdc\n :target: https://www.codacy.com/app/arivers/vica?utm_source=github.com&utm_medium=referral&utm_content=USDA-ARS-GBRU/vica&utm_campaign=Badge_Grade\n\n\nAuthors\n-------\n* Adam R. Rivers, US Department of Agriculture, Agricultural Research Service\n* Qingpeng Zhang, US Department of Energy, Joint Genome Institute\n* Susannah G. Tringe, US Department of Energy, Joint Genome Institute\n\nIntroduction\n------------\n\nVica is designed to identify highly divergent viruses and phage representing new\nfamilies or orders in assembled metagenomic and metatranscriptomic data. Vica\ndoes this by combining information from across the spectrum of composition\nto homology. The current version of Vica uses three feature sets (5-mers,\ncodon usage in all three frames, and minhash sketches from long kmers (k=24,31).\nThe classifier uses a jointly trained deep neural network and logistic model\nimplemented in Tensorflow. The software is designed to identify both DNA\nand RNA viruses and phage in metagenomes and metatranscriptomes.\n\nModels\n------\n\nThe current leases does not include trained models but we will be adding them\nin the future to allow for the rapid identification of viruses without model training.\n\nUsage\n-----\n\nThis package can classify assembled data and train new classification models.\nMost users will only use the classification functionality in Vica. We will provide\ntrained models for classifying contigs in future releases. classification can be\neasily invoked with the command::\n\n vica classify -infile contigs.fasta -out classifications.txt -modeldir modeldir\n\nThe package also has a suite of tools to prepare data, train and evaluate new\nclassification models. Many of the workflows for doing this can be evoked with\nthe same sub-command interface::\n\n vica split\n vica get_features\n vica train\n vica evaluate\n\nFor details see the Tutorial.\n\nRequirements\n------------\n\nThe package relies on a number of python dependencies that are resolved when\nthe package is installed with PIP.\n\nThe non-python dependencies are:\n\n- Bbtools > v37.75- https://jgi.doe.gov/data-and-tools/bbtools/\n- Prodigal > v2.6.3 - https://github.com/hyattpd/Prodigal\n- GNU Coreutils - http://www.gnu.org/software/coreutils/coreutils.html\n\nDocumentation\n-------------\nDocumentation for the package is at http://vica.readthedocs.io/en/latest/\n\nPackage availability\n--------------------\n- PyPi: https://pypi.python.org/pypi/vica\n- Github: https://github.com/USDA-ARS-GBRU/vica\n\n\nCopyright information\n---------------------\n\nViCA Copyright (c) 2018, The Regents of the University of California, through\nLawrence Berkeley National Laboratory (subject to receipt of any required\napprovals from the U.S. Dept. of Energy). All rights reserved.\n\nIf you have questions about your rights to use or distribute this software,\nplease contact Berkeley Lab's Innovation & Partnerships Office at IPO@lbl.gov\nreferring to \" Viral Classification Algorithm Using Supervised Learning (LBNL\nRef 2017-125).\"\n\nNOTICE. This software was developed under funding from the U.S. Department of\nEnergy. As such, the U.S. Government has been granted for itself and others\nacting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in\nthe Software to reproduce, prepare derivative works, and perform publicly and\ndisplay publicly. The U.S. Government is granted for itself and others acting\non its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the\nSoftware to reproduce, prepare derivative works, distribute copies to the\npublic, perform publicly and display publicly, and to permit others to do so.\n\n\n", "description_content_type": "", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "http://github.com/usda-ars-gbru/vica", "keywords": "virus classifier metagenome RNA DNA microbiome tensorflow", "license": "License :: OSI Approved :: BSD License", "maintainer": "", "maintainer_email": "", "name": "vica", "package_url": "https://pypi.org/project/vica/", "platform": "", "project_url": "https://pypi.org/project/vica/", "project_urls": { "Homepage": "http://github.com/usda-ars-gbru/vica" }, "release_url": "https://pypi.org/project/vica/0.1.5/", "requires_dist": [ "tensorflow (>=1.4)", "pandas (>=0.20.3)", "numpy (>=1.14)", "biopython (>=1.70)", "scipy (>=0.19.0)", "khmer (>=2.1.1)", "ete3", "pyfaidx (>=0.5)", "pyyaml", "scikit-learn (>=0.19.0)" ], "requires_python": ">3.5", "summary": "find highly divergent DNA and RNA viruses in microbiomes", "version": "0.1.5" }, "last_serial": 3677168, "releases": { "0.1.3": [ { "comment_text": "", "digests": { "md5": "d00a11161dd5cf06fa5aa63c752b70f0", "sha256": "63e7a8065d6023228a09457f62c8bfa3cb4230cb88a6a50e401bfd07c8a369d3" }, "downloads": -1, "filename": "vica-0.1.3-py3-none-any.whl", "has_sig": false, "md5_digest": "d00a11161dd5cf06fa5aa63c752b70f0", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": ">3.5", "size": 26505, "upload_time": "2017-12-15T18:53:23", "url": "https://files.pythonhosted.org/packages/00/1c/addca69a6d1b886a04a1f8dd50601339d2e10ceb58574b6defe61a8e493a/vica-0.1.3-py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "da35071e7767c5272ee57a7eead344aa", "sha256": "929bc57eab444f7a677cbb68f6cf4531b4bb586a56e1853cb5f84c9d44cdf393" }, "downloads": -1, "filename": "vica-0.1.3.tar.gz", "has_sig": false, "md5_digest": "da35071e7767c5272ee57a7eead344aa", "packagetype": "sdist", "python_version": "source", "requires_python": ">3.5", "size": 27053, "upload_time": "2017-12-15T18:53:25", "url": "https://files.pythonhosted.org/packages/ec/3b/5f9fb0f845c47f0713861a88add3930c415c2d7bb8d6fcac487533f1acce/vica-0.1.3.tar.gz" } ], "0.1.4": [ { "comment_text": "", "digests": { "md5": "dd93b439a200f93dd8bedcdb359c6f79", "sha256": "487907625f51a208f604357ae6222228911ec2f209a341d4e22853905a0631d7" }, "downloads": -1, "filename": "vica-0.1.4-py3-none-any.whl", "has_sig": false, "md5_digest": "dd93b439a200f93dd8bedcdb359c6f79", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": ">3.5", "size": 29386, "upload_time": "2017-12-19T20:14:09", "url": "https://files.pythonhosted.org/packages/b8/0e/154db270f42f8f4e891311abbb0ca55f0b462255b5fa67ab28e614f0d15e/vica-0.1.4-py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "abb90c2e9fc32a273b4946d5dbe4e95f", "sha256": "d3a4034f23e6915449507fe568d6ac69de12af19d0412a3321ad7102b1c778c6" }, "downloads": -1, "filename": "vica-0.1.4.tar.gz", "has_sig": false, "md5_digest": "abb90c2e9fc32a273b4946d5dbe4e95f", "packagetype": "sdist", "python_version": "source", "requires_python": ">3.5", "size": 30111, "upload_time": "2017-12-19T20:14:11", "url": "https://files.pythonhosted.org/packages/08/35/815df83b6dbb207b771f1fb91d99849b883581845997bcfe2d239cf2de03/vica-0.1.4.tar.gz" } ], "0.1.5": [ { "comment_text": "", "digests": { "md5": "68e16afb4971b2646886d8ba6a1a3530", "sha256": "14721ebdfeff07ee6db967a50b601548e9d7d40430fcf63c7d06cd2bcc11ae9e" }, "downloads": -1, "filename": "vica-0.1.5-py3-none-any.whl", "has_sig": false, "md5_digest": "68e16afb4971b2646886d8ba6a1a3530", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": ">3.5", "size": 66554, "upload_time": "2018-03-16T18:24:40", "url": "https://files.pythonhosted.org/packages/d7/b2/1553cbabc0e96d0b93117c5e295b13b389b19f79c5dd3302f78ee3ce9e6e/vica-0.1.5-py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "dd3f103cbb076bf04e64a2c356f4009d", "sha256": "011a5b16f97cddd2a926d1baf6ea66d625436bfc31fca9a461390c0c7eb4f25f" }, "downloads": -1, "filename": "vica-0.1.5.tar.gz", "has_sig": false, "md5_digest": "dd3f103cbb076bf04e64a2c356f4009d", "packagetype": "sdist", "python_version": "source", "requires_python": ">3.5", "size": 70354, "upload_time": "2018-03-16T18:24:55", "url": "https://files.pythonhosted.org/packages/aa/84/4f6404c068355d2e6e88ecad7464ed3a74d100ffc8470730b2e582ceface/vica-0.1.5.tar.gz" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "68e16afb4971b2646886d8ba6a1a3530", "sha256": "14721ebdfeff07ee6db967a50b601548e9d7d40430fcf63c7d06cd2bcc11ae9e" }, "downloads": -1, "filename": "vica-0.1.5-py3-none-any.whl", "has_sig": false, "md5_digest": "68e16afb4971b2646886d8ba6a1a3530", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": ">3.5", "size": 66554, "upload_time": "2018-03-16T18:24:40", "url": "https://files.pythonhosted.org/packages/d7/b2/1553cbabc0e96d0b93117c5e295b13b389b19f79c5dd3302f78ee3ce9e6e/vica-0.1.5-py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "dd3f103cbb076bf04e64a2c356f4009d", "sha256": "011a5b16f97cddd2a926d1baf6ea66d625436bfc31fca9a461390c0c7eb4f25f" }, "downloads": -1, "filename": "vica-0.1.5.tar.gz", "has_sig": false, "md5_digest": "dd3f103cbb076bf04e64a2c356f4009d", "packagetype": "sdist", "python_version": "source", "requires_python": ">3.5", "size": 70354, "upload_time": "2018-03-16T18:24:55", "url": "https://files.pythonhosted.org/packages/aa/84/4f6404c068355d2e6e88ecad7464ed3a74d100ffc8470730b2e582ceface/vica-0.1.5.tar.gz" } ] }