get promoter by extend from gencode gtf file

get_promoter_by_extend.r

#!/usr/bin/env Rscript
docstring <- "Usage: ./get_promoter_by_extend.r <encode_gtf> <extend> <output>"
args <- docopt::docopt(docstring)
args$extend <- as.numeric(args$extend)
print(args)
suppressPackageStartupMessages({
    library(tidyverse)
    library(magrittr)
    library(rtracklayer)
})
# args <- list(
#     encode_gtf = "gencode.vM23.chr_patch_hapl_scaff.annotation.gtf",
#     extend = 2000,
#     output = "promoter_2000.bed"
# )
cli::cli_alert_info("reading gtf")
gtf <- rtracklayer::import.gff(args$encode_gtf)
cli::cli_alert_success("read gtf done")
gene_df <- as_tibble(gtf) %>%
    filter(type == "gene") %>%
    select(c(seqnames, start, end, gene_name, score, strand)) %>%
    mutate(score = 0)

tss_df <- gene_df %>%
    mutate(end = start + 1)

promoter_df <- tss_df %>%
    mutate(start = start - args$extend, end = end + args$extend)
# filter mainchr
promoter_df <- promoter_df %>%
    filter(seqnames %>% str_detect("^chr(\\d{1,2}|X|Y)$"))

promoter_df %>% write_tsv(
    args$output,
    col_names = FALSE
)