| ... | ... |
@@ -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{
|
