{ "info": { "author": "Greene Lab", "author_email": "team@greenelab.com", "bugtrack_url": null, "classifiers": [ "Environment :: Web Environment", "Intended Audience :: Developers", "Intended Audience :: Science/Research", "License :: OSI Approved :: BSD License", "Operating System :: OS Independent", "Programming Language :: Python", "Programming Language :: Python :: 2.7", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "===================\nAnnotation Refinery\n===================\n\nThe Annotation Refinery python package consists of functions that process\npublicly available annotated sets of genes, such as Gene Ontology and Disease\nOntology terms.\n\n\nConfiguration files\n-------------------\n\nThe Annotation Refinery requires at least two ``.ini`` configuration files in\nthe main directory to run:\n\n1. A ``main_config.ini`` file with the main configuration settings, and\n\n2. At least one ``.ini`` file, which will contain the locations of\n the desired annotation files for that species, amon other things. Users can\n add configuration files in the main directory for as many species as\n they want the refinery to process.\n\n\nOptionally, there can also be a ``secrets.ini`` file, which stores values like\nusernames and passwords for access to restricted URLs.\n\n\nThe Main Configuration File\n~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nThe main configuration file includes settings like the location(s) of the\nspecies file(s), where the output of the refinery (the processed genesets)\nshould be loaded to, where annotation files should be downloaded to, \nand optionally, the location of the secrets file.\n\n.. code-block::\n\n [main]\n SECRETS_FILE: secrets.ini\n PROCESS_TO: Tribe\n\n\n # All other download folders in this files should be folders within\n # this root folder\n [download_folder]\n BASE_DOWNLOAD_FOLDER: download_files\n\n\n [Tribe parameters]\n TRIBE_URL: https://tribe.greenelab.com\n\n\n [species files]\n SPECIES_FILES: human.ini\n\n\nThe Species File(s)\n~~~~~~~~~~~~~~~~~~~\n\nEach species file should contain the URLs of the desired annotation files to be\ndownloaded.\n\n.. code-block::\n\n # File for human settings\n\n [species_info]\n SCIENTIFIC_NAME: Homo sapiens\n TAXONOMY_ID: 9606\n SPECIES_DOWNLOAD_FOLDER: download_files/Human\n\n\n # ***********************************************\n # Below, add as sections the types of annotations\n # that should be downloaded and processed\n # ***********************************************\n\n [GO]\n DOWNLOAD: TRUE\n\n GO_OBO_URL: ftp://ftp.geneontology.org/go/ontology/obo_format_1_2/gene_ontology.1_2.obo\n ASSOC_FILE_URL: ftp://ftp.geneontology.org/go/gene-associations/gene_association.goa_human.gz\n\n EVIDENCE_CODES: EXP, IDA, IPI, IMP, IGI, IEP\n\n TAG_MAPPING_FILE: tag_mapping_files/brenda-gobp-all_mapping.dir.v2.txt\n GO_ID_COLUMN: 2\n GO_NAME_COLUMN: 3\n TAG_COLUMN: 1\n TAG_FILE_HEADER: TRUE\n\n\n [KEGG]\n DOWNLOAD: TRUE\n KEGG_ROOT_URL: http://rest.kegg.jp\n DB_INFO_URL: /info/kegg\n SETS_TO_DOWNLOAD: /link/hsa/pathway, /link/hsa/module, /link/hsa/disease\n SET_INFO_DIR: /get/\n\n # This is the type of gene identifier used by KEGG for this species\n XRDB: Entrez\n\n [DO]\n DOWNLOAD: TRUE\n DO_OBO_URL: http://sourceforge.net/p/diseaseontology/code/HEAD/tree/trunk/HumanDO.obo?format=raw\n MIM2GENE_URL: http://omim.org/static/omim/data/mim2gene.txt\n GENEMAP_URL: http://data.omim.org/downloads//genemap.txt\n\n # This is the type of gene identifier used by DO\n XRDB: Entrez\n\n TAG_MAPPING_FILE: tag_mapping_files/tissue-disease_curated-associations.txt\n DO_ID_COLUMN: 2\n DO_NAME_COLUMN: 3\n TAG_COLUMN: 1\n TAG_FILE_HEADER: TRUE\n\n\nThe Secrets File\n~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nThe secrets file contains things like usernames and passwords for databases,\nsecret keys for APIs where annotation files will be downloaded from, etc.\n\n.. code-block::\n\n [OMIM API secrets]\n SECRET_KEY: ExampleSecretKey\n\n [Tribe secrets]\n TRIBE_ID: asdf1234\n TRIBE_SECRET: qwerty1234\n\n USERNAME: example_username\n PASSWORD: password\n\n\nInstructions for getting an OMIM API secret key can be found here:\nhttp://omim.org/downloads\n\nInstructions for getting the Tribe secrets can be found here:\nhttp://tribe-greenelab.readthedocs.io/en/latest/api.html#creating-new-resources-through-tribe-s-api", "description_content_type": null, "docs_url": null, "download_url": null, "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://bitbucket.org/greenelab/annotation-refinery", "keywords": null, "license": "LICENSE.txt", "maintainer": null, "maintainer_email": null, "name": "annotation-refinery", "package_url": "https://pypi.org/project/annotation-refinery/", "platform": "UNKNOWN", "project_url": "https://pypi.org/project/annotation-refinery/", "project_urls": { "Homepage": "https://bitbucket.org/greenelab/annotation-refinery" }, "release_url": "https://pypi.org/project/annotation-refinery/1.0.2/", "requires_dist": null, "requires_python": null, "summary": "Portable Python package to process publicly available annotated sets of genes, such as Gene Ontology and Disease Ontologyterms.", "version": "1.0.2" }, "last_serial": 2331992, "releases": { "1.0.1": [ { "comment_text": "", "digests": { "md5": "bf323644357c9946f841ca49cc456c6a", "sha256": "ce3f06fc985d03755d9c91d3bac99ef282e8604d4d7eeb8781ee4fb78b240302" }, "downloads": -1, "filename": "annotation-refinery-1.0.1.tar.gz", "has_sig": false, "md5_digest": "bf323644357c9946f841ca49cc456c6a", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 37077, "upload_time": "2016-09-08T17:56:06", "url": "https://files.pythonhosted.org/packages/c7/cb/055e78874f8112f10a74f8a2ebc56a961431c495f18a8c528a18e6544a3d/annotation-refinery-1.0.1.tar.gz" } ], "1.0.2": [ { "comment_text": "", "digests": { "md5": "1c7dbd44817031233941ce404a8fee81", "sha256": "64e2b12b315ad3ba05781f614fabafa7ba07e5e63d69f0d7806c294fe8227a8f" }, "downloads": -1, "filename": "annotation-refinery-1.0.2.tar.gz", "has_sig": false, "md5_digest": "1c7dbd44817031233941ce404a8fee81", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 36881, "upload_time": "2016-09-08T18:01:48", "url": "https://files.pythonhosted.org/packages/0f/24/406739cfe0bde3b2e6a2dbdca25325d48f583bd60415a62b11ba7bf5742d/annotation-refinery-1.0.2.tar.gz" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "1c7dbd44817031233941ce404a8fee81", "sha256": "64e2b12b315ad3ba05781f614fabafa7ba07e5e63d69f0d7806c294fe8227a8f" }, "downloads": -1, "filename": "annotation-refinery-1.0.2.tar.gz", "has_sig": false, "md5_digest": "1c7dbd44817031233941ce404a8fee81", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 36881, "upload_time": "2016-09-08T18:01:48", "url": "https://files.pythonhosted.org/packages/0f/24/406739cfe0bde3b2e6a2dbdca25325d48f583bd60415a62b11ba7bf5742d/annotation-refinery-1.0.2.tar.gz" } ] }