view scripts/config_assertions.R @ 2:e20001675838 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 82a0fd493f5866b3ef65019709ae5c865998f802

#!/usr/bin/env R
##
## Sanity Check Methods
##
checkNoMissingRanges <- function(format, barcodes){
    #' Checks coverage of barcodes across all specified ranges
    #'
    #' e.g. 1-50, 60-80 -- barcodes 51-59 are not specified. This
    #'       is not a fatal error, but a warning is issued.
    #'
    #' @param format barcode range and the batches they map to
    #' @param barcodes full list of barcodes
    #' @return list of specified barcodes
    ranges <- c()
    res <- sapply(names(format), function(key){
        rng <- as.integer(unlist(strsplit(key, '-')))
        ranges <<- c(ranges, seq(rng[1],rng[2]))
    })
    full.range <- seq(min(ranges),max(ranges))
    not.in <- !(full.range %in% ranges)
    if (sum(not.in) != 0) {
        message("Warning: values[",
                paste(full.range[not.in], collapse=","),
                "] -> barcodes[",
                paste(barcodes[not.in], collapse=","),
                "] are not used."
                )
    } else {
        message("All barcodes accounted for.")
    }
    return(barcodes[!not.in])
}


checkNoMissingBarcodes <- function(headers, barcodes){
    #' Extracts barcodes in the headers and compares them with those in barcodes
    #'
    #' @param headers matrix headers, must be of P1_B2_ACTG format
    #' @param barcodes full list of barcodes
    barcs.in.matrix <- unique(sort(sub("^.*_([ACTGN]+)$", "\\1", headers)))
    not.in <- !(barcs.in.matrix %in% barcodes)
    if (sum(not.in) > 0){
        message("Warning: Barcodes in matrix not in barcodes file\n", barcs.in.matrix[not.in])
    } else {
        message("All input matrix barcodes accounted for.")
    }
}

checkBatchNamesAreValid <- function(headers){
    #' Checks that Plate and Batch names follow good conventions
    #' i.e. Batch names are NOT reused across plates
    #'
    #' @param headers matrix headers in P1_B2_ACTG format
    plate.and.batch <- unique(sub("^(.*)_([ATCGN]+)$", "\\1", headers))
    message("Discovered ", length(plate.and.batch), " batches: ", paste(plate.and.batch, collapse=" "))

    batch.only <- sub("^.*_(B\\d+)$", "\\1", plate.and.batch)
    dupes.batches <- batch.only[duplicated(batch.only)]

    if (length(dupes.batches) > 0){
        stop("Batches ", paste(dupes.batches, collapse=" "), " have duplicate names in other plates!")
    }
}


assertNoMissingBatches <- function(format, plates){
    #' Checks the barcode and plate spec match
    #'
    #' These must specify the same batches.
    #'
    #' @param format barcode format, ranges to batches
    #' @param plates plate format, plates to batches
    #' @return number of batches
    batches.form = c()
    batches.plate = c()
    for (form in format){batches.form = c(batches.form, form)}
    for (plate in plates){
        batches.plate = c(batches.plate, plate)
    }

    if (length(batches.plate) != length(batches.form)){
        stop("Error: The number of batches specified in the plate do not match those given in the barcode format")
    }

    #range.form <- seq(min(batches.form), max(batches.form))
    range.form <- unique(sort(batches.form))
    range.plate <- unique(sort(batches.plate))

    if (sum(!(range.form %in% batches.form)) > 0){
        stop("Error: Missing batch in barcode format")
    }
    if (sum(!(range.plate %in% batches.plate)) > 0){
        stop("Error: Missing batch in plate format")
    }
    return(length(range.form))
}

sanityCheck <- function(spec, matrix.headers){
    #' Checks specification and matrix headers for consistency
    #'
    #' @param spec experiment specification
    #' @param matrix.headers column names of input matrix
    #' @return list of barcodes, as well as number of barcodes, plates, and batches
    barcodes <- scan(spec$barcodes, what="", sep="\n")
    num.barcodes <- length(barcodes)
    num.plates <- length(names(spec$plate))

    used.barcodes <- checkNoMissingRanges(spec$format, barcodes)
    num.batches <- assertNoMissingBatches(spec$format, spec$plates)
    checkNoMissingBarcodes(matrix.headers, used.barcodes)
    checkBatchNamesAreValid(matrix.headers)

    return(list(barc=barcodes, barc.n=num.barcodes, plates.n=num.plates, batch.n=num.batches))
}