R/import.R

In tanaylab/repguide: Design CRISPR guide RNAs against DNA repetitive sequences

importTEs <- function(filepath = 'path to UCSC RMSK file')
{
  if (!is.null(filepath))
  {
    # Import
    ucsc_rmsk <-
      fread(filepath) %>% 
      as_tibble %>%
      dplyr::rename(chrom = genoName, start = genoStart, end = genoEnd, bin = '#bin') %>%
      arrange(chrom, start, end)
    
    # Adjust 0/1-based coordinates
    ucsc_rmsk_adj <-
      ucsc_rmsk %>%
      mutate(start = start + 1)
      
    colnames(ucsc_rmsk_adj) <- tolower(colnames(ucsc_rmsk_adj))
    
    # Make GRanges
    ucsc_rmsk_gr <- GenomicRanges::makeGRangesFromDataFrame(ucsc_rmsk_adj, keep.extra.columns = TRUE)
    
    # Filter overlapping coords 
    ucsc_rmsk_filt_gr <- ucsc_rmsk_gr[!GenomicRanges::countOverlaps(ucsc_rmsk_gr) > 1, ]
    
    # Add unique TE ID
    ucsc_rmsk_filt_gr$te_id <- 0:(length(ucsc_rmsk_filt_gr) - 1)
  }
  
  return(ucsc_rmsk_filt_gr)
}

importKmers <- function(filepath = 'path to bowtie mapped kmers')
{
  # Import
  kmers <- 
    fread(filepath)[order(V1), ] %>% 
    as_tibble %>%
    dplyr::rename(kmer_id = V1, strand = V2, chrom = V3, start = V4, seq = V5, n_mappings = V6, mismatches = V7) %>%
    mutate(start = start + 1, # adjust for difference between 0-based bowtie and 1-based GRanges
           end = start + nchar(seq) - 1,
           n_mappings = n_mappings + 1) %>%
    replace_na(list(mismatches = 0))
  
  if (nrow(kmers) > 5e7 & parallel::detectCores() > 20)
  {
    print ('Parallel GRanges conversion')
    kmers_gr <- makeGRangesFromDataFramePar(kmers, keep.extra.columns = TRUE)  
  } else {
    kmers_gr <- makeGRangesFromDataFrame(kmers, keep.extra.columns = TRUE)
  }
 
  return(kmers_gr)
}

.importOrNot <- function(variable, genome)
{
  if (class(variable) == 'character')
  {
    if (!fs::is_file(variable)) { stop ('tes, cis, black/whitelist must be path to existing bed file or GRanges object') }
    if (grepl('bed.gz$', variable) | grepl('.bed$', variable)) 
    { 
      variable <- rtracklayer::import.bed(variable) 
    } else {
      variable <- importTEs(variable) 
    }
  }
   
  if (class(variable) == 'GRanges')
  {
    seqlevels(variable, pruning.mode = 'coarse') <- seqlevels(genome)    
  } 

  if (is.null(variable))
  {
    variable <- GRanges()
  }
  return(variable)
}