| ... | ... |
@@ -30,10 +30,10 @@ getInfos <- function(file=NULL, printInfos = TRUE, returnInfos = FALSE) {
|
| 30 | 30 |
}else{
|
| 31 | 31 |
stop("File is not found!")
|
| 32 | 32 |
} |
| 33 |
- file_name <- stringr::str_split(file, "/", simplify = TRUE)[ |
|
| 34 |
- length(stringr::str_split(file, "/", simplify = TRUE))] |
|
| 33 |
+ file_name <- paste0(GetFileName(file), ".", GetFileExtension(file)) |
|
| 35 | 34 |
file_path <- stringr::str_remove(file, paste0(file_name,"$")) |
| 36 |
- if (! stringr::str_detect(file_path, "^[\\.]{0,1}/")) {
|
|
| 35 |
+ if (! stringr::str_detect(file_path, "^[\\.]{0,1}/") &&
|
|
| 36 |
+ .Platform$OS.type != "windows") {
|
|
| 37 | 37 |
file_path <- paste0("./",file_path)
|
| 38 | 38 |
} |
| 39 | 39 |
if(GetFileExtension(file) == "hic"){
|
| ... | ... |
@@ -72,7 +72,13 @@ dir.create(temp.dir) |
| 72 | 72 |
|
| 73 | 73 |
Hic.url <- "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/7386f953-8da9-47b0-acb2-931cba810544/4DNFIOTPSS3L.hic" |
| 74 | 74 |
HicOutput.pth <- file.path(temp.dir, "Control_HIC.hic") |
| 75 |
-download.file(Hic.url, HicOutput.pth, method = 'auto', extra = '-k') |
|
| 75 |
+HicOutput.pth <- normalizePath(HicOutput.pth) |
|
| 76 |
+if(.Platform$OS.type == "windows"){
|
|
| 77 |
+ download.file(Hic.url, HicOutput.pth, method = 'auto', extra = '-k',mode="wb") |
|
| 78 |
+}else{
|
|
| 79 |
+ download.file(Hic.url, HicOutput.pth, method = 'auto', extra = '-k') |
|
| 80 |
+} |
|
| 81 |
+ |
|
| 76 | 82 |
``` |
| 77 | 83 |
|
| 78 | 84 |
## Genomic location and annotation data |
| ... | ... |
@@ -79,14 +79,27 @@ dir.create(temp.dir) |
| 79 | 79 |
```{r, eval = TRUE, message = FALSE}
|
| 80 | 80 |
Hic.url <- "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/7386f953-8da9-47b0-acb2-931cba810544/4DNFIOTPSS3L.hic" |
| 81 | 81 |
HicOutput.pth <- file.path(temp.dir, "Control_HIC.hic") |
| 82 |
-download.file(Hic.url, HicOutput.pth, method = 'auto', extra = '-k') |
|
| 82 |
+HicOutput.pth <- normalizePath(HicOutput.pth) |
|
| 83 |
+if(.Platform$OS.type == "windows"){
|
|
| 84 |
+ download.file(Hic.url, HicOutput.pth, method = "auto", |
|
| 85 |
+ extra = "-k", mode="wb") |
|
| 86 |
+}else{
|
|
| 87 |
+ download.file(Hic.url, HicOutput.pth, method = "auto", extra = "-k") |
|
| 88 |
+} |
|
| 89 |
+ |
|
| 83 | 90 |
``` |
| 84 | 91 |
|
| 85 | 92 |
### Heat shock condition (.mcool File) |
| 86 | 93 |
```{r, eval = TRUE, message = FALSE}
|
| 87 | 94 |
Mcool.url <- "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/4f1479a2-4226-4163-ba99-837f2c8f4ac0/4DNFI8DRD739.mcool" |
| 88 | 95 |
McoolOutput.pth <- file.path(temp.dir, "HeatShock_HIC.mcool") |
| 89 |
-download.file(Mcool.url, McoolOutput.pth, method = "auto", extra = "-k") |
|
| 96 |
+McoolOutput.pth <- normalizePath(McoolOutput.pth) |
|
| 97 |
+if(.Platform$OS.type == "windows"){
|
|
| 98 |
+ download.file(Mcool.url, McoolOutput.pth, method = "auto", |
|
| 99 |
+ extra = "-k", mode="wb") |
|
| 100 |
+}else{
|
|
| 101 |
+ download.file(Mcool.url, McoolOutput.pth, method = "auto", extra = "-k") |
|
| 102 |
+} |
|
| 90 | 103 |
``` |
| 91 | 104 |
|
| 92 | 105 |
## 2 Genomic location and annotation data |
