moth_form

moth_form.R

#' Format a text file for mothur
#'
#' @param fl chr string for input file
#' @param rev_cmp logical if file needs reverse complemeNT
#' @param savefl logical if output file is saved, otherwise the output is returned in the console
moth_form <- function(fl, rev_cmp = FALSE, savefl = TRUE, flnm = 'myfile.txt'){

  # import file
  dat <- read.table(fl, sep = '\t')
  
  # format
  dat <- mutate(dat, 
    V1 = 'barcode', 
    V3 = 'NONE'
    ) %>% 
    select(V1, V2, V3, V6)
  
  # take reverse comp if T
  if(rev_cmp){

    # take reverse complement
    revcd <- as.character(dat$V2) %>% 
      strsplit(., '') %>% 
      lapply(., function(x) paste(rev(x), collapse = '')) %>% 
      unlist %>% 
      chartr("ATGC", "TACG", .)
    
    # replace columns
    dat <- mutate(dat, 
      V2 = 'NONE', 
      V3 = revcd
      )
    
  }

  # return the data if savefl F    
  if(!savefl) return(dat)
  
  write.table(dat, flnm, sep = '\t', quote = F, row.names = F, col.names = F)
  
}