library(tidyverse)
library(rtracklayer)
library(readxl)

gtf <- rtracklayer::import("/net/waxman-server/mnt/data/waxmanlabvm_home/mpyatkov/search_track/09_RefSeqLncRNA76k_ExonCollapsed.gtf")
tmp <- gtf %>% as_tibble()
notation <- read_xlsx("/net/waxman-server/mnt/data/waxmanlabvm_home/mpyatkov/search_track/NOTATION_CONVERSION.xlsx", col_names = T)

tmp <- gtf %>% 
  as_tibble() %>% 
  mutate(gene_id_new = case_when(str_detect(gene_id, "lnc_") ~ paste0("lnc", str_extract(gene_id, "([[:digit:]]+)$")),
                                 T ~ gene_id)) %>% 
  select(-gene_id) %>% 
  select(gene_id = gene_id_new, everything()) %>% 
  mutate(transcript_id = gene_id) %>% 
  relocate(gene_id, .before = transcript_id)  
  

rtracklayer::export(tmp, "/net/waxman-server/mnt/data/waxmanlabvm_home/mpyatkov/search_track/76K_EC_short_name.gtf")