getRepeatMask.R

#!/bin/env Rscript

library(RMySQL)
library(dplyr)
library(stringr)
library(readr)

conn <- dbConnect(MySQL(),
                user='genome',
                dbname='hg38',
                host='genome-mysql.cse.ucsc.edu')
bedFile <- 'repUCSC.bed'
df <- dbSendQuery(conn,'select genoName,genoStart,genoEnd,
                  repName,swScore, strand,
                  repClass, repFamily from rmsk') %>%
        dbFetch(n=-1) %>%
        mutate(genoName = str_replace(genoName,'chr','')) %>%
        tbl_df %>%
        write_tsv(bedFile,col_names=F)
message('written ',bedFile)
dbDisconnect(conn)