pr2_update_all <- import(file_pr2_update_excel, sheet = "pr2", guess_max=200000, na=c("", "-"))

pr2_update <- pr2_update_all %>% 
  filter(REVISION != "TO BE DONE")

  str_c("Number of sequences : ", nrow(pr2_update))

  pr2_missing <-  filter(pr2_update, !(genbank_accession %in% pr2_18S$genbank_accession)) 
  DT::datatable(pr2_missing, caption = "Updated sequences that are not present in PR2 ")
  
  # Use this data frame to download new sequences and then restart from beginning
  accessions <- pr2_missing %>% 
    pull(genbank_accession)
  
  saveRDS(accessions, full_path("accessions_new.rds"))
  
  # export(pr2_missing, full_path("pr2_radiolaria_not_genbank.xlsx"))

  pr2_update <- pr2_update %>% 
    filter(!(genbank_accession) %in% pr2_missing$genbank_accession) 

  str_c("Number of sequences in Genbank : ", nrow(pr2_update))

  filter(pr2_18S, !!as.symbol(target_level) %in% target_group) %>% 
     DT::datatable(caption = "Sequences of target group in pr2 ") 

  filter(pr2_18S, (genbank_accession %in% pr2_update$genbank_accession)) %>% 
    DT::datatable(caption = "Sequences of PR2 that need update")
  
  filter(pr2_update, (genbank_accession %in% pr2_18S_removed$genbank_accession)) %>% 
     DT::datatable(caption = "Updated sequences that are not active in PR2")
  
  filter(pr2_update, !(genbank_accession %in% pr2_18S$genbank_accession))%>% 
     DT::datatable(caption = "Updated sequences that are not present in PR2 ")
  
  left_join(select(pr2_update, genbank_accession), 
            select(pr2_18S, genbank_accession, pr2_accession)) %>% 
   count(genbank_accession) %>% 
   filter(n > 1) %>% 
   DT::datatable(caption = "Sequences updated with 2 entries in PR2  (e.g. with and without introns) ")
  
   filter(pr2_update, !is.na(chimera)) %>% 
     DT::datatable(caption = "Chimera")

pr2_taxo_updated <- pr2_update_all %>% 
  filter(is.na(chimera)) %>% 
  group_by_at(pr2.env$taxo_levels[[8]][4:8]) %>%  
  count() 

pr2_taxo_check(pr2_taxo_updated, pr2.env$taxo_levels[[8]][4:8], full_path("taxo"))

pr2_taxo_updated <- pr2_taxo_updated %>% 
  rename_all(~ str_c(.,"_new" )) %>%
  dplyr::rename(species = species_new) %>% 
  left_join(pr2_taxo) %>% 
  rename_at(pr2.env$taxo_levels[[8]], ~ str_c(.,"_old" )) %>% 
  rename_all( ~ str_replace(.,"_new", "_8" )) %>% 
  dplyr::rename(species_8 = species_old) %>% 
  mutate(kingdom_8 = "Eukaryota",
         supergroup_8 = "Rhizaria",
         division_8 = "Foraminifera",
         domain_9 = kingdom_8,
         supergroup_9 = "TSAR",
         division_9 = supergroup_8,
         subdivision_9 =  division_8,
         class_9 = class_8,
         order_9 = order_8,
         family_9 = family_8, 
         genus_9 = genus_8,
         species_9 = species_8,
         taxo_edited_version = pr2.env$version,
         taxo_edited_by = pr2.env$editor)  
  
export(pr2_taxo_updated, full_path("taxo_updated.xlsx"))

pr2_taxo_not_updated <- pr2_taxo %>% 
  filter(!!as.symbol(target_level) %in% target_group) %>% 
  filter(!(species %in% pr2_taxo_updated$species_8))

export(pr2_taxo_not_updated , full_path("taxo_not_updated.xlsx"))

pr2_update_final <- pr2_update %>% 
  select(genbank_accession, species, eukeref_env_biome) %>% 
  dplyr::rename(species_new = species) %>% 
  left_join(select(pr2_main, pr2_accession, genbank_accession, 
                   removed_version, edited_version, chimera,
                   edited_by, edited_remark,
                   species),
            by = "genbank_accession")

pr2_needs_update <- pr2_update_final %>%  
  filter((species != species_new)|is.na(species)) 

pr2_needs_update %>% 
  DT::datatable(caption = "Actual sequence and pr2_accession needs to be updated  ")

glue::glue("Number of updated sequences  with prior taxonomy: {nrow(filter(pr2_needs_update, !is.na(species)))}")
glue::glue("Number of updated sequences  without prior taxonomy {nrow(filter(pr2_needs_update, is.na(species)))}")

pr2_main_updated <- pr2_update_final %>%  
    select (genbank_accession, 
            species_8 = species_new, 
            species_9 = species_new,
            edited_version,
            edited_by,
            edited_remark,
            removed_version,
            chimera
            ) %>% 
    mutate(edited_version = str_append(edited_version, pr2.env$version) , 
           edited_by = str_append(edited_by, pr2.env$editor)
           # chimera = case_when(!is.na(chimera) ~ 1),
           # chimera_remark = case_when(!is.na(chimera) ~ "chimera detected by M. Sandin"),
           # removed_version = case_when(!is.na(chimera) ~ pr2.env$version,
                                       # TRUE ~ removed_version )
           )