Commit a66e24cd authored by Rauschenberger's avatar Rauschenberger
Browse files

automation

parent 3944a1ae
...@@ -176,13 +176,14 @@ get.snps.bbmri <- function(chr,biobank=NULL,path=getwd(),size=500*10^3){ ...@@ -176,13 +176,14 @@ get.snps.bbmri <- function(chr,biobank=NULL,path=getwd(),size=500*10^3){
file2 <- paste0(study[j],".chr",chr,".dose.vcf") file2 <- paste0(study[j],".chr",chr,".dose.vcf")
# Decompressing missing files in personal folder. # Decompressing missing files in personal folder.
if(!file.exists(file.path(path1,file2))){ #if(!file.exists(file.path(path1,file2))){
file.copy(from=file.path(path0,file0),to=file.path(path1,file1)) # file.copy(from=file.path(path0,file0),to=file.path(path1,file1))
R.utils::gunzip(filename=file.path(path1,file1),remove=TRUE,overwrite=TRUE) # R.utils::gunzip(filename=file.path(path1,file1),remove=TRUE,overwrite=TRUE)
} #}
# Reading in files. # Reading in files.
vcf <- vcfR::read.vcfR(file=file.path(path1,file2),skip=skip[i],nrows=size,verbose=FALSE) #vcf <- vcfR::read.vcfR(file=file.path(path1,file2),skip=skip[i],nrows=size,verbose=FALSE)
vcf <- vcfR::read.vcfR(file=file.path(path0,file0),skip=skip[i],nrows=size,verbose=FALSE)
vcf <- vcf[vcf@fix[,"CHROM"]!="",] # bug fix vcf <- vcf[vcf@fix[,"CHROM"]!="",] # bug fix
vcf@fix[,"ID"] <- paste0(vcf@fix[,"ID"],"_",seq_len(dim(vcf)["variants"])) vcf@fix[,"ID"] <- paste0(vcf@fix[,"ID"],"_",seq_len(dim(vcf)["variants"]))
collect[i,j][[1]] <- vcf collect[i,j][[1]] <- vcf
...@@ -248,9 +249,9 @@ get.snps.bbmri <- function(chr,biobank=NULL,path=getwd(),size=500*10^3){ ...@@ -248,9 +249,9 @@ get.snps.bbmri <- function(chr,biobank=NULL,path=getwd(),size=500*10^3){
} }
# Remove temporary files. # Remove temporary files.
for(j in seq_along(study)){ #for(j in seq_along(study)){
file.remove(file.path(path1,paste0(study[j],".chr",chr,".dose.vcf"))) # file.remove(file.path(path1,paste0(study[j],".chr",chr,".dose.vcf")))
} #}
} }
......
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