R/vFun_prjManager.R

In lucidif/HiCeekR: GUI for Hi-C data analysis

#' makeConfig
#'
#' make HiCeekR config file
#'
#' @param path character vector that contain folder path
#'
#' @return HCRwd.info file that contain the path of HiCeekR woorking directory
#'
#' @keywords internal
#'
#'
#' @examples
#'
makeConfig=function(path=paste0(getwd(),"/")){
    cfMatrix<-matrix(ncol=1,nrow=2)
    cfMatrix[1,1]<-path
    cfMatrix[2,1]<-getwd()
    write.table(cfMatrix, "HCR.config", col.names=FALSE, row.names=FALSE,
                quote=FALSE, sep="\t")
    #print(paste0("working path:",path, ".....setted"))
}



#' setHCRwd
#'
#' set folder in which HiCeekR works
#'
#' @param path character vector that contain folder path
#'
#' @return HCRwd.info file that contain the path of HiCeekR woorking directory
#' @keywords internal
#'
#' @example
#'
setHCRwd=function(path){
    write.table(path,"HCRwd.info", col.names=FALSE, row.names=FALSE,
                quote=FALSE, sep="\t")
    print(paste0("HCRwd path:",path, ".....setted"))
}


#' makeHiCeekRwd
#'
#' make folder in which HiCeekR works
#'
#' @param path character vector that contain folder path
#'
#' @return None
#' @keywords internal
#'
#' @example
#'
makeHCRwd<-function(path = getwd()){
    mainFolder<-paste0(path,"HiCeekRwd/")
    setHCRwd(mainFolder)
    SubFolder_lv1<-c('Projects','RefGenomes','Annotations')
    dir.create (mainFolder, showWarnings=TRUE, recursive=FALSE)
    len<-length(SubFolder_lv1)
    for (ls in 1:len){
        secondSub<-paste0 (mainFolder, SubFolder_lv1[ls], '/')

        dir.create (secondSub, showWarnings=TRUE, recursive=FALSE)


    }
}


#' make HiCeekR project folder
#'
#' make Project folder in which HiCeekR works
#'
#' @param path character vector that contain folder path
#' @param name character vector that defines name of project
#'
#' @return None
#'
#' @keywords internal
#' @example
#'
makeHCRprj=function (name, path){

    ##path<-where you would create a folder with variable 'name' name
    ##quando trova cartelle con lo stesso nome sovrascrive i contenuti o unisce
    ##i contenuti delle cartelle

    ##folderTree structure
    ##-project_folder(sama name variable name)
    ##-----ProjectData
    ##------------Hi-C
    ##------------Epi
    ##------------Exp

    zeroLevel<-'ProjectData'
    ProjectData_SubFolder_lv1<-c('Hi-C','Epi','Other')
    ProjectData_HiCsubFolder_lv2<-c("bam", "matrix")
    #,'Genomes')

    ##when you add new folder in project_folder folder add it to zeroLevel array
    ##and make new array with su folder
    ##Es:   zeroLevel<-c('ProjectData', 'exampleFolder')
    ##      exampleFolder_SubFolder_lv1<- c('example_subfolder1','example_subfolder2','example_subfolder3')
    ##if you wont add a new subfolder in example_subfolder1 add new subsubfolder 1 and 2 in
    ##example_subfolder1_subfolder_lv2<- c('subsubfolder1', 'subsubfolder2')

    mainFolder<- paste0 (path,name, '/')

    dir.create (mainFolder, showWarnings=TRUE, recursive=FALSE)
    lenFirst <- length (zeroLevel)
    lenSecond <- length (ProjectData_SubFolder_lv1)

    for (lf in 1:lenFirst){
        firstSub<-paste0 (mainFolder,zeroLevel[lf],'/')
        dir.create (firstSub, showWarnings=TRUE, recursive=FALSE)
    }

    ##for folder in first folder of zeroLevel insert hear
    ##you need to create new for for every zeroLevel element

    ##for element in ProjectData=====================
    for(ls in 1:lenSecond){
        secondSub<-paste0 (mainFolder,'ProjectData/',
                           ProjectData_SubFolder_lv1[ls], '/')

        dir.create (secondSub, showWarnings=TRUE, recursive=FALSE)


    }
    ##===============================================

    ##for folders in Hi-C
    # for (ls in 1:length(ProjectData_HiCsubFolder_lv2)){
    #     print(paste0(mainFolder, "ProjectData/Hi-C",
    #            ProjectData_HiCsubFolder_lv2[ls], "/"
    #     ))
    #     thirdSud<-paste0(mainFolder, "ProjectData/Hi-C/",
    #                     ProjectData_HiCsubFolder_lv2[ls], "/"
    #                     )
    #
    #     dir.create (thirdSub, showWarnings=TRUE, recursive=FALSE)
    #
    # }


    #=============================================================

}


#' makeHCRan
#'
#' @param name character varible that contain the name of analysis
#' @param prjPath  character variable that contain the path of projects that
#' @param infoTable table that contai analysis information
#'
#' @return
#' @keywords internal
#'
#' @examples
makeHCRan<-function(name, prjPath, infoTable){
    mainFolder<-paste0(prjPath,name,"/")
    dir.create(mainFolder,showWarnings=TRUE, recursive=FALSE)

    lv1<-c("SysOut", "Results")
    lv2<-c("Pre-Processing", "Filtering", "Binning", "Normalization",
            "Downstream", "Visualization", "Report")

    #dir creation
    for(i in 1:length(lv1)){
        lv1path<-paste0(mainFolder,lv1[i],"/")
        dir.create(lv1path)
        for(j in 1:length(lv2)){
            dir.create(paste0(lv1path,lv2[j]))
        }
    }

    #create info file
    #control table
    infoTable<-testInfoTable(infoTable)
    write.table(infoTable,paste0(mainFolder,"info.tsv"),
                sep="\t",
                quote=FALSE,
                col.names=FALSE,
                row.names=TRUE)

}