git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqTools@128661 bc3139a8-67e5-0310-9ffc-ced21a209358
Wolfgang Kaisers authored on 13/04/2017 15:56:51
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## |
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+## ## |
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+## Project : seqTools ## |
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+## Created : 26.August.2013 ## |
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+## Author : W. Kaisers ## |
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+## Version : 0.99.13 ## |
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+## File : simFunctions.r ## |
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+## Content : Functions which produce fastq files with simulated data ## |
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+## (Done for testing Fastqq and DNA k-mer counting) ## |
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+## writeSimFastq, writeSimContFastq, simFastqqRunTimes, ## |
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+## sim_fq ## |
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+## ## |
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## |
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+ |
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## |
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+## Create fastq files with simulated k-mers |
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## |
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+ |
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+writeSimFastq<-function(k=6, nk=5, nSeq=10, filename="sim.fq.gz") |
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+{
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+ # + + + + + + + + + + + + + + + + + + + + + + + + + + + + # |
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+ # k |
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+ # + + + + + + + + + + + + + + + + + + + + + + + + + + + + # |
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+ if(!is.numeric(k)) |
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+ stop("'k' must be numeric.")
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+ if(length(k) != 1) |
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+ stop("'k' must have length 1.")
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+ k <- as.integer(k) |
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+ if( (k < 1) || (k > max_k) ) |
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+ stop("'k' out of range.")
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+ |
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+ # + + + + + + + + + + + + + + + + + + + + + + + + + + + + # |
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+ # nk |
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+ # + + + + + + + + + + + + + + + + + + + + + + + + + + + + # |
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+ if(!is.numeric(nk)) |
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+ stop("'nk' must be numeric.")
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+ if(length(nk) != 1) |
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+ stop("'nk' must have length 1.")
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+ nk<-as.integer(nk) |
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+ if( (nk < 1) || (nk > 1000) ) |
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+ stop("nk must be positive and <1000.")
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+ |
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+ # + + + + + + + + + + + + + + + + + + + + + + + + + + + + # |
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+ # nSeq |
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+ # + + + + + + + + + + + + + + + + + + + + + + + + + + + + # |
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+ if(!is.numeric(nSeq)) |
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+ stop("'nSeq' must be numeric.")
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+ if(nSeq < 1) |
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+ stop("'nSeq' must be positive.")
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+ |
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+ # + + + + + + + + + + + + + + + + + + + + + + + + + + + + # |
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+ # filename |
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+ # + + + + + + + + + + + + + + + + + + + + + + + + + + + + # |
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+ if(!is.character(filename)) |
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+ stop("'filename' must be string.")
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+ |
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+ # + + + + + + + + + + + + + + + + + + + + + + + + + + + + # |
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+ # Do the work |
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+ # + + + + + + + + + + + + + + + + + + + + + + + + + + + + # |
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+ bm <- Sys.localeconv()[7] |
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+ val <- as.integer(c(k, nk, nSeq)) |
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+ |
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+ pseq <- .Call("sim_dna_k_mer", val, PACKAGE="seqTools")
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+ res <- .Call("gzwrite_fastq_dna", val, pseq, filename, PACKAGE="seqTools")
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+ |
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+ message("[writeSimFastq] file '", basename(filename), "': ",
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+ format(res,big.mark=bm), " Bytes written.") |
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+ |
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+ # + + + + + + + + + + + + + + + + + + + + + + + + + + + + # |
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+ # Terminate function. |
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+ # + + + + + + + + + + + + + + + + + + + + + + + + + + + + # |
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+ return(invisible()) |
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+} |
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+ |
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## |
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+## writeSimContFastq |
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## |
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+writeSimContFastq<-function(k=6, nk=5, nSeq=10, pos=1, |
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+ kIndex=1, nContam=nSeq, filename="simc.fq.gz") |
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+{
|
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+ # + + + + + + + + + + + + + + + + + + + + + + + + + + + + # |
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+ # k |
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+ # + + + + + + + + + + + + + + + + + + + + + + + + + + + + # |
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+ if(!is.numeric(k)) |
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+ stop("k must be numeric.")
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+ if(length(k) != 1) |
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+ stop("k must have length 1.")
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+ k<-as.integer(k) |
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+ if( (k < 1) || (k > max_k) ) |
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+ stop("k out of range.")
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+ |
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+ # + + + + + + + + + + + + + + + + + + + + + + + + + + + + # |
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+ # nk |
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+ # + + + + + + + + + + + + + + + + + + + + + + + + + + + + # |
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+ if(!is.numeric(nk)) |
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+ stop("nk must be numeric.")
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+ if(length(nk) != 1) |
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+ stop("nk must have length 1.")
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+ nk<-as.integer(nk) |
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+ if( (nk < 1) || (nk > 1000) ) |
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+ stop("nk must be positive and <1000.")
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+ |
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+ # + + + + + + + + + + + + + + + + + + + + + + + + + + + + # |
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+ # nSeq |
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+ # + + + + + + + + + + + + + + + + + + + + + + + + + + + + # |
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+ if(!is.numeric(nSeq)) |
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+ stop("nSeq must be numeric.")
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+ if(length(nSeq) != 1) |
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+ stop("nSeq must have length 1.")
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+ if(nSeq < 1) |
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+ stop("nSeq must be positive.")
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+ |
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+ # + + + + + + + + + + + + + + + + + + + + + + + + + + + + # |
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+ # pos |
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+ # + + + + + + + + + + + + + + + + + + + + + + + + + + + + # |
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+ if(!is.numeric(pos)) |
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+ stop("pos must be numeric.")
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+ pos<-as.integer(pos) |
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+ if( any(pos < 1) || any(pos > (k * (nk - 1) + 1))) |
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+ stop("pos out of range.")
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+ |
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+ # + + + + + + + + + + + + + + + + + + + + + + + + + + + + # |
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+ # writeSimContFastq should take 1-based positions |
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+ # while "set_dna_k_mer" takes 0-based positions |
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+ # + + + + + + + + + + + + + + + + + + + + + + + + + + + + # |
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+ pos<-pos - 1L |
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+ |
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+ # + + + + + + + + + + + + + + + + + + + + + + + + + + + + # |
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+ # kIndex |
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+ # + + + + + + + + + + + + + + + + + + + + + + + + + + + + # |
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+ if(!is.numeric(kIndex)) |
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+ stop("kIndex must be numeric.")
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+ |
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+ kIndex <- as.integer(kIndex) |
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+ |
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+ if(length(pos) != length(kIndex)) |
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+ stop("pos and kIndex must have equal length.")
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+ |
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+ if( any(kIndex < 1L) || any(kIndex > 4^k) ) |
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+ stop("kIndex out of range.")
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+ |
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+ # + + + + + + + + + + + + + + + + + + + + + + + + + + + + # |
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+ # writeSimContFastq should take 1-based k-indices |
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+ # while "set_dna_k_mer" takes 0-based k-indices |
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+ # + + + + + + + + + + + + + + + + + + + + + + + + + + + + # |
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+ kIndex <- kIndex - 1L |
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+ |
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+ # + + + + + + + + + + + + + + + + + + + + + + + + + + + + # |
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+ # nContam: Deterministic replacements are copied |
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+ # into the first 'nContam' reads |
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+ # + + + + + + + + + + + + + + + + + + + + + + + + + + + + # |
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+ if(!is.numeric(nContam)) |
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+ stop("nContam must be integer.")
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+ |
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+ nContam <- as.integer(nContam) |
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+ |
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+ if(length(nContam) != 1) |
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+ stop("nContam must have length 1.")
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+ |
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+ if( (nContam < 1) || (nContam > nSeq) ) |
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+ stop("nContam must be >0 and <nSeq.")
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+ |
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+ # + + + + + + + + + + + + + + + + + + + + + + + + + + + + # |
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+ # filename |
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+ # + + + + + + + + + + + + + + + + + + + + + + + + + + + + # |
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+ if(!is.character(filename)) |
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+ stop("filename must be character.")
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+ |
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+ # + + + + + + + + + + + + + + + + + + + + + + + + + + + + # |
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+ # Do the work |
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+ # + + + + + + + + + + + + + + + + + + + + + + + + + + + + # |
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+ bm <- Sys.localeconv()[7] |
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+ |
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+ val <- as.integer(c(k, nk, nSeq)) |
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+ |
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+ pseq <- .Call("sim_dna_k_mer", val, PACKAGE="seqTools")
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+ |
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+ prseq <- .Call("set_dna_k_mer",
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+ val, pseq,pos, kIndex, nContam, PACKAGE="seqTools") |
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+ |
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+ res <- .Call("gzwrite_fastq_dna",
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+ val, prseq, filename, PACKAGE="seqTools") |
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+ |
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+ message("[writeSimContFastq] file '", basename(filename),
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+ "': ", format(res,big.mark=bm), " Bytes written.") |
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+ |
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+ # + + + + + + + + + + + + + + + + + + + + + + + + + + + + # |
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+ # Terminate function |
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+ # + + + + + + + + + + + + + + + + + + + + + + + + + + + + # |
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+ return(invisible()) |
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+} |
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+ |
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+ |
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+ |
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+simFastqqRunTimes<-function(k, nSeq, filedir=".") |
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+{
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+ if(missing(k)) |
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+ k <- 2:(max_k) |
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+ else |
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+ {
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+ if(!is.numeric(k)) |
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+ stop("'k' must be numeric.")
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+ |
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+ k <- sort(unique(as.integer(k))) |
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+ |
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+ if(any(k < 1) || any(k > max_k)) |
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+ stop("'k' out of range.")
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+ } |
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+ |
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+ if(missing(nSeq)) |
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+ nSeq <- as.integer(c(1e2, 1e3, 1e4, 1e5, 1e6, 1e7)) |
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+ else {
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+ if(!is.numeric(nSeq)) |
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+ stop("'nSeq' must be numeric.")
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+ nSeq <- as.integer(nSeq) |
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+ if(any(nSeq < 1) ) |
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+ stop("'nSeq' must be positive.")
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+ } |
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+ |
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+ if(!is.character(filedir)) |
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+ stop("'filedir' must be character.")
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+ |
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+ if(!file.exists(filedir)) |
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+ {
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+ if(!dir.create(filedir)) |
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+ stop("Cannot create filedir '", filedir, "'.")
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+ } |
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+ |
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+ # + + + + + + + + + + + + + + + + + + + + + + + + + + + + # |
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+ # Write simulated fastq files |
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+ # + + + + + + + + + + + + + + + + + + + + + + + + + + + + # |
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+ message("[simFastqqRunTimes] Creating fastq files:")
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+ fqFiles <- character(length(nSeq)) |
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+ bm <- Sys.localeconv()[7] |
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+ |
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+ for(j in 1:length(nSeq)) |
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+ {
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+ fqFiles[j] <- file.path(filedir, |
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+ paste("sfqrt_nSeq", nSeq[j], ".fq.gz", sep=""))
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+ |
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+ message("[simFastqqRunTimes] (",format(j , w=3),"/", length(nSeq),
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+ ") nSeq=", format(nSeq[j], big.mark=bm, w=12)) |
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+ |
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+ # Allways equal sized reads: k=6, read length=102 |
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+ writeSimFastq(k=6, nk=17, nSeq=nSeq[j], filename=fqFiles[j]) |
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+ } |
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+ |
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+ # + + + + + + + + + + + + + + + + + + + + + + + + + + + + # |
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+ # Prepare result table |
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+ # + + + + + + + + + + + + + + + + + + + + + + + + + + + + # |
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+ nSim <- length(k) * length(nSeq) |
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+ m <- 1 |
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+ res<-data.frame(id=1:nSim, k=0, nSeq=0, runtime=0) |
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+ |
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+ for(i in 1:length(k)) |
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+ {
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+ for(j in 1:length(nSeq)) |
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+ {
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+ message("[simFastqqRunTimes] (",
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+ format(m, width=3),"/", nSim, ") Fastqq run.") |
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+ |
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+ fq <- fastqq(fqFiles[j], k=k[i]) |
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+ res$k[m] <- k[i] |
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+ res$nSeq[m] <- nSeq[j] |
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+ res$runtime[m] <- collectDur(fq) |
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+ m <- m + 1 |
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+ } |
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+ } |
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+ return(res) |
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+} |
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+ |
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+ |
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## |
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+## Encapsulates whole simulation studies |
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## |
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+ |
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+sim_fq<-function(nRep=2, nContamVec=c(100, 1000), grSize=20, nSeq=1e4, |
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+ k=6, kIndex=1365, pos=20) |
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+{
|
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| 281 |
+ ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## |
|
| 282 |
+ ## Arguments |
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| 283 |
+ ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## |
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+ |
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+ # nContam : Absolute number of contaminated sequences |
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+ # grSize : Nr of fastq files in control and contamination group |
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+ # nSeq : Nr of reads per fastq file |
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+ # k : k-mer length used in fastqq function |
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+ # kIndex : k-mer index of contaminating sequence default is "CCCCCC" |
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+ # pos : Contamination is inserted at position in read sequence, |
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+ # default is 20 |
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+ |
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+ if(length(kIndex) != length(pos)) |
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+ stop("'kIndex' and 'pos' must have equal length.")
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+ |
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| 296 |
+ ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## |
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| 297 |
+ |
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| 298 |
+ |
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| 299 |
+ ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## |
|
| 300 |
+ ## Fixed internal values |
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| 301 |
+ ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## |
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+ |
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+ # ksim : k-mer sized used for simulation |
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+ ksim <- 6 |
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+ # nksim : number of k-mers per read (determines read length) |
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| 306 |
+ nksim <- 17 |
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| 307 |
+ |
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| 308 |
+ |
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| 309 |
+ ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## |
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| 310 |
+ ## Write simulated fastq files for control group |
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| 311 |
+ ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## |
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+ |
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+ # ctrl_vec=leaf labels for control group |
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| 314 |
+ ctrl_vec <- 1:grSize |
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+ ctrl_files <- paste("sfq_i", ctrl_vec, "_ctrl.fq.gz", sep = "")
|
|
| 316 |
+ |
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| 317 |
+ for(i in ctrl_vec){
|
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+ writeSimFastq(k=ksim, nk=nksim, nSeq=nSeq, |
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| 319 |
+ filename = ctrl_files[i]) |
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| 320 |
+ } |
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| 321 |
+ |
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| 322 |
+ ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## |
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| 323 |
+ ## Prepare values for contamination and result |
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| 324 |
+ ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## |
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| 325 |
+ |
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+ # cont_vec=leaf labels for contamination group |
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| 327 |
+ # (must be nonoverlapping with ctrl_vec) |
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| 328 |
+ cont_vec <- ctrl_vec + 100 |
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| 329 |
+ contamVecLen <- length(nContamVec) |
|
| 330 |
+ nSim = nRep * contamVecLen |
|
| 331 |
+ # Result data.frame |
|
| 332 |
+ res <- data.frame(id=1:nSim, nContam=0, rep=0, sum=NA) |
|
| 333 |
+ |
|
| 334 |
+ m <- 1 |
|
| 335 |
+ for(i in 1:length(nContamVec)) |
|
| 336 |
+ {
|
|
| 337 |
+ nContam<-nContamVec[i] |
|
| 338 |
+ for(j in 1:nRep) |
|
| 339 |
+ {
|
|
| 340 |
+ message("[sim_fq] Simulation (",
|
|
| 341 |
+ format(m, width=3), "/", nSim, ").") |
|
| 342 |
+ |
|
| 343 |
+ cont_files <- paste("sfq_i", cont_vec, "_cont.fq.gz", sep="")
|
|
| 344 |
+ |
|
| 345 |
+ for(i in 1:length(cont_vec)) |
|
| 346 |
+ writeSimContFastq(k=ksim, nk=nksim, nSeq=nSeq, pos=pos, |
|
| 347 |
+ nContam=nContam, kIndex=kIndex, |
|
| 348 |
+ filename=cont_files[i]) |
|
| 349 |
+ |
|
| 350 |
+ ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## |
|
| 351 |
+ ## read Fastqq |
|
| 352 |
+ ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## |
|
| 353 |
+ ctrl_fqq <- fastqq(ctrl_files, k=k) |
|
| 354 |
+ probeLabel(ctrl_fqq) <- ctrl_vec |
|
| 355 |
+ cont_fqq <- fastqq(cont_files, k=k) |
|
| 356 |
+ probeLabel(cont_fqq) <- cont_vec |
|
| 357 |
+ |
|
| 358 |
+ ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## |
|
| 359 |
+ ## merge, dist, hclust |
|
| 360 |
+ ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## |
|
| 361 |
+ mrg <- mergeFastqq(ctrl_fqq, cont_fqq) |
|
| 362 |
+ mtx <- cbDistMatrix(mrg) |
|
| 363 |
+ hc <- hclust(as.dist(mtx)) |
|
| 364 |
+ |
|
| 365 |
+ ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## |
|
| 366 |
+ ## Calculate results and write into res |
|
| 367 |
+ ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## |
|
| 368 |
+ res$nContam[m] <- nContam |
|
| 369 |
+ res$rep[m] <- j |
|
| 370 |
+ |
|
| 371 |
+ ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## |
|
| 372 |
+ ## Calculate how many labels of the contamination group |
|
| 373 |
+ ## are in the first half of leaf labels |
|
| 374 |
+ ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## |
|
| 375 |
+ res$sum[m] <- sum(hc$order[ctrl_vec] > grSize) |
|
| 376 |
+ m <- m + 1 |
|
| 377 |
+ } |
|
| 378 |
+ } |
|
| 379 |
+ res$lat <- pmin(res$sum, grSize - res$sum) / grSize * 100 |
|
| 380 |
+ res$perc <- res$nContam / nSeq * 100 |
|
| 381 |
+ return(res) |
|
| 382 |
+} |
|
| 383 |
+ |
|
| 384 |
+ |
|
| 385 |
+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## |
|
| 386 |
+## END OF FILE |
|
| 387 |
+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## |