Metadata-Version: 1.1
Name: annotation-refinery
Version: 1.0.2
Summary: Portable Python package to process publicly available annotated sets of genes, such as Gene Ontology and Disease Ontologyterms.
Home-page: https://bitbucket.org/greenelab/annotation-refinery
Author: Greene Lab
Author-email: team@greenelab.com
License: LICENSE.txt
Description: ===================
        Annotation Refinery
        ===================
        
        The Annotation Refinery python package consists of functions that process
        publicly available annotated sets of genes, such as Gene Ontology and Disease
        Ontology terms.
        
        
        Configuration files
        -------------------
        
        The Annotation Refinery requires at least two ``.ini`` configuration files in
        the main directory to run:
        
        1. A ``main_config.ini`` file with the main configuration settings, and
        
        2. At least one ``<species>.ini`` file, which will contain the locations of
           the desired annotation files for that species, amon other things. Users can
           add configuration files in the main directory for as many species as
           they want the refinery to process.
        
        
        Optionally, there can also be a ``secrets.ini`` file, which stores values like
        usernames and passwords for access to restricted URLs.
        
        
        The Main Configuration File
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        The main configuration file includes settings like the location(s) of the
        species file(s), where the output of the refinery (the processed genesets)
        should be loaded to, where annotation files should be downloaded to, 
        and optionally, the location of the secrets file.
        
        .. code-block::
        
            [main]
            SECRETS_FILE: secrets.ini
            PROCESS_TO: Tribe
        
        
            # All other download folders in this files should be folders within
            # this root folder
            [download_folder]
            BASE_DOWNLOAD_FOLDER: download_files
        
        
            [Tribe parameters]
            TRIBE_URL: https://tribe.greenelab.com
        
        
            [species files]
            SPECIES_FILES: human.ini
        
        
        The Species File(s)
        ~~~~~~~~~~~~~~~~~~~
        
        Each species file should contain the URLs of the desired annotation files to be
        downloaded.
        
        .. code-block::
        
            # File for human settings
        
            [species_info]
            SCIENTIFIC_NAME: Homo sapiens
            TAXONOMY_ID: 9606
            SPECIES_DOWNLOAD_FOLDER: download_files/Human
        
        
            # ***********************************************
            # Below, add as sections the types of annotations
            # that should be downloaded and processed
            # ***********************************************
        
            [GO]
            DOWNLOAD: TRUE
        
            GO_OBO_URL: ftp://ftp.geneontology.org/go/ontology/obo_format_1_2/gene_ontology.1_2.obo
            ASSOC_FILE_URL: ftp://ftp.geneontology.org/go/gene-associations/gene_association.goa_human.gz
        
            EVIDENCE_CODES: EXP, IDA, IPI, IMP, IGI, IEP
        
            TAG_MAPPING_FILE: tag_mapping_files/brenda-gobp-all_mapping.dir.v2.txt
            GO_ID_COLUMN: 2
            GO_NAME_COLUMN: 3
            TAG_COLUMN: 1
            TAG_FILE_HEADER: TRUE
        
        
            [KEGG]
            DOWNLOAD: TRUE
            KEGG_ROOT_URL: http://rest.kegg.jp
            DB_INFO_URL: /info/kegg
            SETS_TO_DOWNLOAD: /link/hsa/pathway, /link/hsa/module, /link/hsa/disease
            SET_INFO_DIR: /get/
        
            # This is the type of gene identifier used by KEGG for this species
            XRDB: Entrez
        
            [DO]
            DOWNLOAD: TRUE
            DO_OBO_URL: http://sourceforge.net/p/diseaseontology/code/HEAD/tree/trunk/HumanDO.obo?format=raw
            MIM2GENE_URL: http://omim.org/static/omim/data/mim2gene.txt
            GENEMAP_URL: http://data.omim.org/downloads/<SecretKey>/genemap.txt
        
            # This is the type of gene identifier used by DO
            XRDB: Entrez
        
            TAG_MAPPING_FILE: tag_mapping_files/tissue-disease_curated-associations.txt
            DO_ID_COLUMN: 2
            DO_NAME_COLUMN: 3
            TAG_COLUMN: 1
            TAG_FILE_HEADER: TRUE
        
        
        The Secrets File
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        The secrets file contains things like usernames and passwords for databases,
        secret keys for APIs where annotation files will be downloaded from, etc.
        
        .. code-block::
        
            [OMIM API secrets]
            SECRET_KEY: ExampleSecretKey
        
            [Tribe secrets]
            TRIBE_ID: asdf1234
            TRIBE_SECRET: qwerty1234
        
            USERNAME: example_username
            PASSWORD: password
        
        
        Instructions for getting an OMIM API secret key can be found here:
        http://omim.org/downloads
        
        Instructions for getting the Tribe secrets can be found here:
        http://tribe-greenelab.readthedocs.io/en/latest/api.html#creating-new-resources-through-tribe-s-api
        
Platform: UNKNOWN
Classifier: Environment :: Web Environment
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
