mysql.auto.build: Build anor database in mysql (auto from...

In JhuangLab/annovarR: Integrated Framework to Annotate Genetic Variants

Description

Build anor database in mysql (auto from extdata/config/database.toml)

Usage

mysql.auto.build(
  anno.name = "",
  buildver = "hg19",
  database.dir = "/path/",
  mysql.connect.params = list(user = "", password = "", host = "localhost", port =
    "3306"),
  overwrite = FALSE,
  append = FALSE,
  index = "chr_start_index",
  db.type = "mysql",
  database.cfg = system.file("extdata", "config/databases.toml", package = "anor"),
  extra_fread_params = list(sep = "\t", header = TRUE, return_1L = FALSE),
  mysql.build.params = list(fread.params = list(sep = "\t")),
  batch_lines = 1e+07,
  start_index = 1,
  new.colnames = NULL,
  verbose = TRUE
)

Arguments

anno.name	Annotation name, eg. avsnp138, avsnp147, 1000g2015aug_all
buildver	Genome version, hg19, hg38, mm10 and others
database.dir	Dir of the databases
mysql.connect.params	Mysql parameters, [host, dbname, table.name, user, password etc.]
overwrite	Logical indicating wheather overwrite sqlite database, default is FALSE
append	Logical indicating wheather append the data to sqlite database, default is FALSE
index	Index name in sqlite
db.type	Setting the database type (sqlite, txt or mysql)
database.cfg	Configuration file of anor databases infomation
extra_fread_params	Pass to batch_file, default is to get value from database.cfg
mysql.build.params	Extra params pass to mysql.build
batch_lines	Parameters pass to batch_file, default is 10000000
start_index	default is 1, control the skip rows, n = (i-1) * batch_lines
new.colnames	Use the fread determined colnames or use new colnames
verbose	Logical indicating wheather print the extra log infomation

Examples

i <- 'hg19_avsnp147'
database <- system.file('extdata', sprintf('demo/%s.txt', i), package = 'anor')
file.copy(database, sprintf('%s/%s.txt', tempdir(), i))
## Not run: 
 mysql.auto.build(anno.name = 'avsnp147', database.dir = tempdir(), 
 mysql.connect.params = list(user = 'username', password = 'password', 
 host = 'localhost', port = 3306, dbname = 'anor'))

## End(Not run)

JhuangLab/annovarR documentation built on April 23, 2020, 10:51 p.m.