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-

-## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

-##                                                                           ##

-##  Project   :   seqTools                                                   ##

-##  Created   :   26.August.2013                                             ##

-##  Author    :   W. Kaisers                                                 ##

-##  File      :   kMer.r                                                     ##

-##  Content   :   Functionality for counting DNA k-mers                      ##

-##                (independent of fastq or fasta files)                      ##

-##                countKmers, countDnaKmers, revCountDnaKmers,               ##

-##                countGenomeKmers, countSpliceKmers                         ##

-## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

-

-

-## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

-## Counts DNA k-mers on specified regions inside single (character) sequence

-## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

-countDnaKmers <- function(dna, k, start=1, width=nchar(dna) - k + 1)

-{

-    if(!is.character(dna))

-        stop("'dna' must be character.")

-    

-    if(length(dna) != 1)

-        stop("'dna' must have length 1.")

-    

-    if(is.numeric(start))

-        start <- as.integer(start)

-    

-    if(is.numeric(width))

-        width <- as.integer(width)

-    

-    if(length(width) == 1)

-        width <- rep(width, length(start))

-    

-    if(is.numeric(k))

-        k <- as.integer(k)

-    

-    if(length(k)!=1)

-        stop("'k' must have length 1.")

-    

-    if(k < 1)

-        stop("'k' must be positive.")

-    

-    if(k > max_k)

-        stop("'k' must not exceed", max_k, ".")

-  

-    nc <- nchar(dna)

-    if(k > nc)

-        stop("'k' must be <= nchar(dna).")

-    if(any(start + width + k > nc + 2))

-        stop("Search region exceeds string end.")

-  

-    ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

-    ## Counts N's

-    ## ToDo: Return value

-    ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

-    nn <- integer(length(start))

-    return(.Call("count_dna_Kmers", 

-                            dna, start, width, k, nn, PACKAGE="seqTools"))

-    

-}

-

-

-## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

-## Counts DNA k-mers on specified regions inside single (character) sequence 

-## in reverse direction

-## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

-revCountDnaKmers <- function(dna, k, start, width)

-{

-    if(!is.character(dna))

-        stop("'dna' must be character.")

-    

-    if(length(dna) != 1)

-        stop("'dna' must have length 1.")

-    

-    if(is.numeric(start))

-        start <- as.integer(start)

-    

-    if(is.numeric(width))

-        width <- as.integer(width)

-    

-    if(length(width) == 1)

-        width <- rep(width, length(start))

-    

-    if(length(width) != length(start))

-        stop("'width' must have length 1 or the same length as 'start'.")

-    

-    if(is.numeric(k))

-        k <- as.integer(k)

-    

-    if(any(width + k > start))

-        stop("'width' must be <=  'start' - 'k'.")

-    

-    ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

-    ## nn contains N counts

-    ## ToDo: Add value of nn to returned object

-    ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

-    nn <- integer(length(start))

-    

-    return(.Call("rev_count_dna_Kmers",

-                            dna, start, width, k, nn, PACKAGE="seqTools"))

-}

-

-

-## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

-## Counts DNA k-mers on specified regions inside multiple (character) sequences

-## in possibly reversed direction (depending on strand)

-## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

-countGenomeKmers <- function(dna, seqid, start, width, strand, k)

-{

-    if(!is.character(dna))

-        stop("'dna' must be character.")

-    

-    if(!is.numeric(seqid))

-        seqid <- as.integer(seqid)

-    rg <- range(seqid)

-    

-    if(rg[1] < 0)

-        stop("Negative seqid's are not allowed.")

-    

-    if(rg[2] > length(dna))

-        stop("Out of range seqid's.")

-    

-    if(!is.numeric(start))

-        stop("'start' must be numeric.")

-    start <- as.integer(start)

-    

-    if(!is.numeric(width))

-        stop("'width' must be numeric")

-    width <- as.integer(width)

-    

-    if(is.factor(strand))

-        strand <- as.integer(strand)

-    else

-    {

-        if(!is.numeric("strand"))

-            strand <- as.integer(strand)        

-    }

-    

-    nStart <- length(start)

-    if( (length(seqid) != nStart) | (length(width) != nStart) |

-                (length(strand) != nStart) )

-        stop("'seqid', 'start', 'width' and 'strand' must have same length.")

-    

-    if(length(k) != 1)

-        stop("'k' must be a single value.")

-    

-    if(!is.numeric(k))

-        stop("'k' must be numeric.")

-    k<-as.integer(k)

-    

-    if(k <= 0)

-        stop("'k' must be >=1")

-    

-    if(k > max_k)

-        stop("'k' must not exceed", max_k, ".")

-    

-    ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

-    ## Counts N's

-    ## ToDo: Return value

-    ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

-    nn <- integer(length(start))

-    return(.Call("count_genome_Kmers", dna, seqid, start, width,

-                            strand, k, nn, PACKAGE="seqTools"))

-}

-

-

-## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

-## Counts DNA k-mers on each border of a splice-site defined by wLend and 

-## wRstart in range of size width

-## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

-

-countSpliceKmers <- function(dna, seqid, lEnd, rStart, width, strand, k)

-{

-    if(!is.character(dna))

-        stop("'dna' must be character.")

-    

-    if(!is.numeric(seqid))

-        stop("'seqid' must be numeric.")

-    seqid <- as.integer(seqid)

-    

-    rg <- range(seqid)

-    if(rg[1] < 0)

-        stop("Negative seqid's are not allowed.")

-    

-    if(rg[2] > length(dna))

-        stop("Out of range seqid's.")

-    

-    if(!is.numeric(lEnd))

-        stop("'lEnd' must be numeric.")

-    lEnd <- as.integer(lEnd)

-    

-    if(!is.numeric(rStart))

-        stop("'rStart' must be numeric.")

-    rStart <- as.integer(rStart)

-    

-    if(!is.numeric(width))

-        stop("'width' must be numeric.")

-    width <- as.integer(width)

-    

-    if(is.factor(strand))

-        strand <- as.integer(strand)

-    else

-    {

-        if(!is.numeric("strand"))

-            strand <- as.integer(strand)        

-    }

-    

-    nStart <- length(lEnd)

-    if(length(seqid) != nStart | length(rStart) != nStart | 

-             length(width) != nStart | length(strand) != nStart)

-    {

-        stop(paste("'seqid', 'lEnd', 'rStart', 'width'",

-                            "and 'strand' must have equal length."))

-    }

-    if(!is.numeric(k))

-        stop("'k' must be numeric.")

-    k <- as.integer(k)

-    

-    if(length(k) != 1)

-        stop("'k' must be a single value.")

-    

-    if(k > max_k)

-        stop("'k' must not exceed", max_k, ".")

-    

-    ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

-    ## Plus strand

-    ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

-    plus_strand<-strand == 1

-    

-    if(sum(plus_strand) > 0)

-    {

-        if(any((lEnd[plus_strand] - width[plus_strand] - k + 1) < 0))

-            stop("lEnd must be >= width+k-1 for all +-strand coordinates")

-    }

-    

-    ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

-    ## Counts N's

-    ## ToDo: Return value

-    ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

-    nn <- integer(length = nStart)

-    

-    return(.Call("count_splice_Kmers", dna, seqid, lEnd, rStart, width, 

-                            strand, k, nn, PACKAGE="seqTools")) 

-}

-

-

-## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

-## END OF FILE

-## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##