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+

+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

+##                                                                           ##

+##  Project   :   seqTools                                                   ##

+##  Created   :   26.August.2013                                             ##

+##  Author    :   W. Kaisers                                                 ##

+##  File      :   fastaFunctions.r                                           ##

+##  Content   :   Functions which work on fastq and fastq and write output   ##

+##                files: writeFai,  countFastaKmers                          ##

+##                                                                           ##

+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

+

+writeFai <- function(infiles, outfiles)

+{

+    if(!is.character(infiles))

+        stop("infiles must be character.")

+    

+    if(!is.character(outfiles))

+        stop("outfiles must be character.")

+    

+    if(length(infiles) != length(outfiles))

+        stop("infiles and outfiles must have equal length.")

+    

+    if(any( !file.exists(infiles) ) )

+        stop("Some infile(s) do not exist!\n")

+    

+    .Call("write_fai", infiles, outfiles, PACKAGE = "seqTools")

+    message("[write_fai] done.\n")

+    

+    return(invisible())

+}

+

+

+countFastaKmers <- function(filenames, k=4)

+{

+    if(!is.character(filenames))

+        stop("filenames must be character.")

+    

+    if(!is.numeric(k))

+        stop("k must be numeric.")

+    k <- as.integer(k)

+    

+    if( (k < 0) || (k > max_k) )    

+        stop("k must be in range 0,    ... , ", max_k, ".")

+    

+    res <- .Call("count_fasta_Kmers", filenames, k, PACKAGE="seqTools")

+    

+    return(res)

+}

+

+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

+## END OF FILE

+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##