R/abifToFastq.R

In CrispRVariants: Tools for counting and visualising mutations in a target location

#'Read a file in ab1 (Sanger) format and convert to fastq
#'
#'This is an R implementation of Wibowo Arindrarto's abifpy.py trimming module,
#'which itself implement's Richard Mott's trimming algorithm
#'See \url{https://github.com/bow/abifpy} for more details.
#'
#'Requires Bioconductor package SangerseqR
#'@param seqname name of sequence, to appear in fastq file
#'@param fname filename of sequence in ab1 format
#'@param outfname filename to append the fastq output to
#'@param trim should low quality bases be trimmed from the ends?  TRUE or FALSE
#'@param cutoff probability cutoff
#'@param min_seq_len minimum number of sequenced bases required in order to trim
#'the read
#'@param offset phred offset for quality scores
#'@param recall Use sangerseqR to resolve the primary sequence if two sequences
#'are present.  May cause quality scores to be ignored. (Default: FALSE)
#'@author Helen Lindsay
#'@return None.  Sequences are appended to the outfname.
#'@examples
#'ab1_fname <- system.file("extdata", "IM2033.ab1", package = "CrispRVariants")
#'abifToFastq("IM2033", ab1_fname, "IM2033.fastq")
#'@export
abifToFastq <- function(seqname, fname, outfname, trim = TRUE, cutoff = 0.05,
                        min_seq_len = 20, offset = 33, recall = FALSE){
    sangerseqr <- requireNamespace("sangerseqR")
    stopifnot(isTRUE(sangerseqr))

    # Translation of python function
    abif <- sangerseqR::read.abif(fname)
    if (is.null(abif@data$PCON.2)){
       message(sprintf("failed on %s", seqname))
       return()
    }

    # Remove the extra character if it exists
    nucseq <- substring(abif@data$PBAS.2, 1, length(abif@data$PLOC.2))

    # sangerSeqR PCON.2 is a UTF8-encoded character vector in release, 
    # an integer vector in devel
    if (! typeof(abif@data$PCON.2) == "integer"){
        num_quals <- utf8ToInt(abif@data$PCON.2)[1:length(abif@data$PLOC.2)]
    } else {
        num_quals <- abif@data$PCON.2[1:length(abif@data$PLOC.2)]
    }
  
    if (isTRUE(recall)){
        recalled <- sangerseqR::makeBaseCalls(sangerseqR::sangerseq(abif))
        nucseq <- sangerseqR::primarySeq(recalled, string = TRUE)
        if (nchar(nucseq) != length(num_quals)){
            trim <- FALSE
            # Set all quality scores equal
            num_quals <- rep(60, nchar(nucseq)) 
            # 60 is compatible with all phred offsets, according
            #  to Wikipedia Sanger scores do not usually exceed 60
            warning("Length of quality scores does not equal length of
                    re-called base sequence, ignoring quality scores")
        }
    }
  
    if (trim == FALSE){
        writeFastq(outfname, list("seqname" = seqname, "seq" = nucseq,
                  "quals" = rawToChar(as.raw(num_quals + offset))))
        return()
    }

    trim_msg <- paste("Sequence %s can not be trimmed because",
                      "it is shorter than the trim segment size")
    if (nchar(nucseq) <= min_seq_len){
        warning(sprintf(trim_msg, seqname))
        return()
    }

    scores = cutoff - 10^(num_quals / -10)
    running_sum <- rep(0, length(scores) + 1)

    # Note running_sum counts from zero, scores from 1
    for (i in 1:length(scores)){
        num <- scores[i] + running_sum[i]
        running_sum[i+1] <- ifelse(num < 0, 0, num)
    }

    trim_start <- min(which(running_sum > 0)) - 1
    trim_finish <- which.max(running_sum) - 2
    # -1 for running_sum offset, -1 because python doesn't include ends

    # Additional check that there is enough sequence (not in abifpy):
    if (trim_finish - trim_start < min_seq_len -1){
        warning(sprintf(trim_msg, seqname))
        return()
    }

    writeFastq(outfname, list("seqname" = seqname,
        "seq" = substring(nucseq, trim_start, trim_finish),
        "quals" = rawToChar(as.raw(num_quals[trim_start:trim_finish]+offset))))
  
    return()
}