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