#' Removes sequences shorter than a given cutoff
#' @inheritParams applyOperation
#' @export
binSizeCheck <- function(all_results, config)
{
op_number <- config$current_op_number
op_args <- config$operation_list[[op_number]]
op_full_name <- paste(op_number, op_args$name, sep = '_')
op_dir <- file.path(config$output_dir, config$base_for_names, op_full_name)
dir.create(op_dir, showWarnings = FALSE, recursive = TRUE)
data_source_indx <- grep(op_args$data_source, names(all_results))
stopifnot(length(data_source_indx) == 1)
seq_dat <- all_results[[data_source_indx]]$seq_dat
per_read_metrics <- data.frame(seq_name = as.character(seq_dat@id),
stringsAsFactors = F)
per_read_metrics$pid <- gsub('^.*PID:([ACGT]*)_([ACGT]*).*$', '\\1\\2', per_read_metrics$seq_name)
n_per_pid <- data.frame(table(per_read_metrics$pid))
n_per_pid$Var1 <- as.character(n_per_pid$Var1)
names(n_per_pid) <- c('pid', 'seq_left')
per_read_metrics <- merge(per_read_metrics, n_per_pid,
all.x=TRUE, by.x = 'pid',
by.y = 'pid')
seq_dat <- seq_dat[order(as.character(seq_dat@id))]
per_read_metrics <- per_read_metrics[order(per_read_metrics$seq_name),]
min_bin_size <- op_args$min_bin_size
if (is.null(min_bin_size))
{
min_bin_size <- 3
}
trim_steps <- list(step1 = list(name = 'seq_left',
threshold = min_bin_size,
comparator = `>=`,
breaks = c(Inf, min_bin_size+c(1,0,-1), -Inf)
)
)
result <- list(trim_steps = trim_steps,
metrics = list(per_read_metrics = per_read_metrics))
kept_dat <- getKept(result, seq_dat=seq_dat)
class(result) <- 'binSizeCheck'
if (op_args$cache){
result$seq_dat <- kept_dat
}
result$input_dat <- seq_dat
result$config <- list(op_number = op_number,
op_args = op_args,
op_full_name = op_full_name,
op_dir = op_dir)
return(result)
}
saveToDisk.binSizeCheck <- function(result, config, seq_dat)
{
kept <- getKept(result, seq_dat)
trimmed <- getTrimmed(seq_dat = seq_dat, kept_dat = kept)
if (length(kept) > 0)
{
tmp_name <- file.path(result$config$op_dir,
paste(config$base_for_names, '_kept_', result$config$op_args$name, '.fastq', sep = ''))
writeFastq(kept, tmp_name, compress=F)
}
if (length(trimmed) > 0)
{
tmp_name <- file.path(result$config$op_dir,
paste(config$base_for_names, '_trimmed_', result$config$op_args$name, '.fastq', sep = ''))
writeFastq(trimmed, tmp_name, compress=F)
}
return(result)
}
computeMetrics.binSizeCheck <- function(result, config, seq_dat)
{
return(result)
}
print.binSizeCheck <- function(result, config)
{
cat('\n-------------------')
cat('\nOperation: binSizeCheck')
cat('\n-------------------')
cat('\nKept Sequences:\n')
print(result$summary[,c('parameter', 'k_seqs', 'k_mean_length', 'k_mean_qual')])
cat('\n-------------------')
cat('\nTrimmed Sequences:\n')
print(result$summary[,c('parameter', 't_seqs', 't_mean_length', 't_mean_qual')])
invisible(result)
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.