converting ENSEMBL regulatory build GFF file to a regular tab delimited file

ensembl_regulatory_build_to_tab.r

#obtained from ftp://ftp.ensembl.org/pub/grch37/release-87/regulation/homo_sapiens/homo_sapiens.GRCh37.Regulatory_Build.regulatory_features.20161117.gff.gz
#date: 12/01/2017
library(stringr)
library(tidyr)

homo_sapiens.GRCh37.Regulatory_Build.regulatory_features.20161117 <- read.delim("/local/home/mlist/Projects/homo_sapiens.GRCh37.Regulatory_Build.regulatory_features.20161117.gff", header=FALSE)

ensembl_reg_hg19 <- tidyr::separate(homo_sapiens.GRCh37.Regulatory_Build.regulatory_features.20161117, col = V9, into = c("ID", "bound_end", "bound_start", "description", "feature_type"), sep = ";")
apply(ensembl_reg_hg19, 2, function(x) str_replace_all(x, pattern = ".*=", ""))
ensembl_reg_hg19_tidy <- apply(ensembl_reg_hg19, 2, function(x) str_replace_all(x, pattern = ".*=", ""))
ensembl_reg_hg19_tidy <- ensembl_reg_hg19_tidy[, c("V1", "V4", "V5", "ID", "feature_type")]
colnames(ensembl_reg_hg19_tidy) <- c("CHROMOSOME", "START", "END", "ID", "FEATURE")

write.table(ensembl_reg_hg19_tidy, quote=FALSE, sep = "\t", 
            row.names = FALSE,
            file = "ENSEMBL_regulatory_build_hs37d5.txt")