Entering edit mode
4.8 years ago
Shicheng Guo
★
9.4k
Hi All,
I hope to use HGMD to test my algorithm for SNP functional prediction. The problem is I don't know where to download it?
Meanwhile, I tried the following script. However, mysql server doesn't work well. any suggestion?
getHGMDData <- function(geneName,
user='hgmd',
password='hgmd',
host='192.168.99.100',
port='3306',
dbname='hgmd') {
library("DBI")
library("RMySQL")
# load also HGMD
con=dbConnect(MySQL(),username=user,password=password,host=host,unix.socket=port,dbname=dbname)
# get all mutations
res <- dbSendQuery(con,sprintf("select * from mutnomen inner join allmut as h1 on h1.acc_num=mutnomen.acc_num where gene='%s'",geneName))
rawdat<-fetch(res,n=-1)
cleanHGVS <- paste0("c.",rawdat$hgvs[!is.na(rawdat$hgvs)])
dbDisconnect(con)
(list(hgvs=cleanHGVS,rawData=rawdat))
}
getHGMDData("TP53")
Thanks.