R/findPatternPos.R

In BUMHMM: Computational pipeline for computing probability of modification from structure probing experiment data

# BUM-HMM
# Copyright (C) 2016 Alina Selega, Sander Granneman, Guido Sanguinetti

findPatternPos <- function(patterns, sequence, strand) {

    if ((strand != '+') & (strand != '-')) {
        stop("Strand should be either plus or minus, specified with a sign.")
    }
    else if (nchar(sequence) == 0) {
        stop('The sequence should be non-empty.')
    }
    else if (length(patterns) == 0) {
        stop('The list of patterns should be non-empty.')
    }
    else {

        indices <- list()

        ## Find all occurences of patterns in the full sequence
        for (i in 1:length(patterns)) {
            p <- patterns[i]
            indices[i] <- stringi::stri_locate_all_fixed(sequence, p,
                                                         overlap=TRUE)
        }

        ## Compute positions of the middle nucleotide in each pattern occurence
        nuclPosition <- lapply(indices, function(x) x[, 1] +
                                 (ceiling(nchar(patterns[1]) / 2) - 1))

        ## Get rid of naming attributes left from the stringi function
        nuclPosition <- lapply(nuclPosition, function(x)
            if (!(is.null(names(x)))) {unname(x)} else {x})

        ## Annotate found indices by the corresponding pattern
        if (strand == '+') {
            names(nuclPosition) <- patterns
        }

        ## Turn patterns to complementary if working with the minus strand
        if (strand == "-") {
            complPatterns <- list()
            for (i in 1:length(patterns)) {
                chars <- array('')
                for (j in 1:nchar(patterns[i])) {
                    chars[j] <- switch(substr(patterns[i], j, j),
                                     'A' = 'T', 'T' = 'A', 'G' = 'C', 'C' = 'G')
                }
                complPatterns[[i]] <- paste(chars, collapse='')
            }
            ## Annotate found indices by the corresponding pattern
            names(nuclPosition) <- complPatterns
        }

        ## Arrange them in the order of original patterns
        nuclPosition <- nuclPosition[patterns]

        return(nuclPosition)
    }
}