注释精炼器 1.0.2

主要配置文件

主要配置文件包括设置，如物种文件的存储位置、精炼器输出（处理后的基因集）应加载到的位置、注释文件应下载到的位置，以及可选的秘密文件的存储位置。

[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

物种文件

每个物种文件应包含要下载的所需注释文件的URL。

# 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

秘密文件

秘密文件包含数据库的用户名和密码、API的秘密密钥等，从这些API中下载注释文件。

[OMIM API secrets]
SECRET_KEY: ExampleSecretKey

[Tribe secrets]
TRIBE_ID: asdf1234
TRIBE_SECRET: qwerty1234

USERNAME: example_username
PASSWORD: password

获取OMIM API密钥的说明请在此处查看：http://omim.org/downloads

获取Tribe密钥的说明请在此处查看：http://tribe-greenelab.readthedocs.io/en/latest/api.html#creating-new-resources-through-tribe-s-api