Where is the genbank directory in the prism_path

[eastar2016]

The genbank directory is mentioned in line 520 of the PRISM.R, and the files in this directory are used in subsequent code. Can you provide the complete directory or protocols for preparing this directory and related files?

[inspirewind]

The same issue.
Noting that in the prism_genbank function in function.R, the full path of genbank_dict is constructed by concatenating the prism_path parameter from PRISM.R with the fixed string 'genbank/genbank_indices.RDS'.

prism_genbank = function(blast){
  
  genbank_dict = readRDS(paste0(prism_path, 'genbank/genbank_indices.RDS'))
  uacc = unique(blast$sacc)
  fn = genbank_dict$gbfile[unique(genbank_dict$list_indices[genbank_dict$accessions_flat %in% uacc])]
  
  message("Reading GenBank files ...")
  
  genbank = list()
  for(i in seq_along(fn)){
    # message(sprintf("📄 Reading GenBank file %d of %d ...", i, length(fn)))
    genbank[[i]] = readRDS(
      paste0(prism_path, 'genbank/rds/', fn[i], '.RDS')
    ) %>% subset(sacc %in% uacc)
  }

Where is this genbank directory located? Is it the directory where the genbank.zip downloaded from Google Drive is extracted? However, after extraction, this directory only contains an rds folder with separate .rds files, not a merged genbank_indices.RDS. What merging operation should I perform?

[MaohuiY]

@inspirewind The compressed file contains the file genbank_indices.RDS; please check it carefully. Additionally, to run successfully, simply move all RDS files except genbank_indices.RDS into the genbank/rds directory. Best wishes!

[inspirewind]

Thank you for the reminder!

When moving the rds directory to my working dir, I used the wildcard rds/gb*, which caused me to miss genbank_indices.RDS. Thank you for your careful check