sql2sqlite: Convert sql file to sqlite database

In JhuangLab/annovarR: Integrated Framework to Annotate Genetic Variants

Description

Convert sql file to sqlite database

Usage

sql2sqlite(sql.file = "", statements = "", dbname = "", verbose = FALSE, ...)

Arguments

sql.file	SQL file of sqlite database dumped
statements	SQL statements split by ';\n' (small dataset)
dbname	Path of output sqlite database
verbose	Ligical indicating wheather show the log message
...	Other parameters be used in dbSendQuery

Examples

sql.file <- system.file('extdata', 'demo/hg19_avsnp147.sqlite.sql', package = 'anor')
out.sqlite <- tempfile()
sqlite <- Sys.which(c('sqlite3', 'sqlite'))
sqlite <- sqlite[sqlite != ''][1]
sqlite <- unname(sqlite)
if (!is.na(sqlite)) {
  sql2sqlite(sql.file = sql.file, dbname = out.sqlite, 
  verbose = FALSE)
  unlink(out.sqlite)
}
statements <- paste0(readLines(sql.file), collapse = '\n')
sql2sqlite(statements = statements, dbname = out.sqlite, 
verbose = FALSE)
unlink(out.sqlite)

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