#### don't delete the scoring matrix when echoCommand

Ge Tan authored on 24/11/2016 18:59:53
Showing 1 changed files

 ... ... `@@ -3,35 +3,38 @@` 3 3 ` ### Exported!` 4 4 ` scoringMatrix <- function(distance=c("far", "medium", "near")){` 5 5 ` distance <- match.arg(distance)` 6 `- lastzMatrix <- list(medium=matrix(c(91, -114, -31, -123,` 7 `- -114, 100, -125, -31,` 8 `- -31, -125, 100,-114,` 9 `- -123, -31, -114, 91),` 10 `- nrow=4, ncol=4,` 11 `- dimnames=list(c("A", "C", "G", "T"),` 12 `- c("A", "C", "G", "T"))` 13 `- ),` 14 `- far=matrix(c(91, -90, -25, -100,` 15 `- -90, 100, -100, -25,` 16 `- -25, -100, 100, -90,` 17 `- -100, -25, -90, 91),` 18 `- nrow=4, ncol=4,` 19 `- dimnames=list(c("A", "C", "G", "T"),` 20 `- c("A", "C", "G", "T"))` 21 `- ),` 22 `- near=matrix(c(90, -330, -236, -356,` 23 `- -330, 100, -318, -236,` 24 `- -236, -318, 100, -330,` 25 `- -356, -236, -330, 90),` 26 `- nrow=4, ncol=4,` 27 `- dimnames=list(c("A", "C", "G", "T"),` 28 `- c("A", "C", "G", "T"))` 29 `- )` 6 `+ lastzMatrix <- list(` 7 `+ # Default` 8 `+ medium=matrix(c(91, -114, -31, -123,` 9 `+ -114, 100, -125, -31,` 10 `+ -31, -125, 100,-114,` 11 `+ -123, -31, -114, 91),` 12 `+ nrow=4, ncol=4,` 13 `+ dimnames=list(c("A", "C", "G", "T"),` 14 `+ c("A", "C", "G", "T"))` 15 `+ ),` 16 `+ ## HOXD55` 17 `+ far=matrix(c(91, -90, -25, -100,` 18 `+ -90, 100, -100, -25,` 19 `+ -25, -100, 100, -90,` 20 `+ -100, -25, -90, 91),` 21 `+ nrow=4, ncol=4,` 22 `+ dimnames=list(c("A", "C", "G", "T"),` 23 `+ c("A", "C", "G", "T"))` 24 `+ ),` 25 `+ ## human-chimp` 26 `+ near=matrix(c(90, -330, -236, -356,` 27 `+ -330, 100, -318, -236,` 28 `+ -236, -318, 100, -330,` 29 `+ -356, -236, -330, 90),` 30 `+ nrow=4, ncol=4,` 31 `+ dimnames=list(c("A", "C", "G", "T"),` 32 `+ c("A", "C", "G", "T"))` 33 `+ )` 30 34 ` )` 31 35 ` return(lastzMatrix[[distance]])` 32 36 ` }` 33 37 ` ` 34 `-` 35 38 ` ### -----------------------------------------------------------------` 36 39 ` ### lastz wrapper` 37 40 ` ### Exported!` ... ... `@@ -54,7 +57,10 @@ lastz <- function(assemblyTarget, assemblyQuery,` 54 57 ` }` 55 58 ` ` 56 59 ` matrixFile <- tempfile(fileext=".lastzMatrix")` 57 `- on.exit(unlink(matrixFile))` 60 `+ if(!isTRUE(echoCommand)){` 61 `+ ## If echo the command, we keep the scoring matrix file.` 62 `+ on.exit(unlink(matrixFile))` 63 `+ }` 58 64 ` write.table(scoringMatrix(distance), file=matrixFile, quote=FALSE,` 59 65 ` sep=" ", row.names=FALSE, col.names=TRUE)` 60 66 ` ## The options used here is taken from RunLastzChain_sh.txt ` ... ... `@@ -117,7 +123,6 @@ lastz <- function(assemblyTarget, assemblyQuery,` 117 123 ` matrixFile)` 118 124 ` )` 119 125 ` ` 120 `- message("Starting lastz")` 121 126 ` if(is.null(chrsTarget)){` 122 127 ` chrsTarget <- seqnames(seqinfo(TwoBitFile(assemblyTarget)))` 123 128 ` }else{`