R/callSnpSeek-function.R

In Lagaillette/RRicePackage: rRice package to make easier the study of the genomic of rice

#' noDoubleIds
#'
#' This function allows to avoid the problem when the id is composed by 2 ids
#' Example : Os01g0115500,Os01g0115566
#'
#' @param id character
#' @return It will return only one id if it is not a double ID. Otherwise, it
#' will return a list with the both ids
#' @rdname noDoubleIds-function
noDoubleIds <- function (id) { 
    ##print(id[[1]]) -> id
    ##print(id[[2]]) -> msu7Name
    ##print(id)
    msu7Name <- as.character(id[[2]])
    iricname <- as.character(id[[3]])
    id <- as.character(id[[1]])
    
    
    ##for the ids like "Os01g0115500,Os01g0115566" (the double ids)
    ##we only test the first id
    if(grepl(',', id)) 
    {
        ids <- strsplit(id, ",")
        id <- ids[[1]][[1]]
        id1 <- ids[[1]][[2]]
        liste <- list(id,id1)
        return(list(list(id,msu7Name,iricname),list(id1,msu7Name,iricname)))
    }
    else {
        return(list(list(id,msu7Name,iricname)))
    }
}

#' id
#'
#' This function will only return the id from the rOutput 
#' 
#' @param rOutput character
#' @return this funciton will only return the id
#' @importFrom jsonlite fromJSON
#' @rdname id-function
id <- function (rOutput) {
    #output <- getOutPutJSON(rOutput)
    #print(rOutput)
    
    #t <- '{"msu7Name": "LOC_Os01g01970"}' # --> BON
    #t <- "{'msu7Name': 'LOC_Os01g01970'}" # --> PAS BON POUR JSON
    # rOutput <- {'contig': 'chr01',
    #             'fmin': 524578, 
    #             'rappredName': 'None', 
    #             'fmax': 528002, 
    #             'strand': -1, 
    #             'uniquename': 'LOC_Os01g01970', 
    #             'fgeneshName': 'chr01-gene_91', 
    #             'msu7Name': 'LOC_Os01g01970', 
    #             'description': 'expressed protein', 
    #             'raprepName': 'Os01g0109750', 
    #             'iricname': 'OsNippo01g015950'}
    
    ##A VOIR AVEC BAPTISTE POUR QUE JE RECOIVE UN BON JSON
    rOutput <- gsub('\'', '"', rOutput)
    rOutput <- gsub('None', '"None"', rOutput)
    
    #print(j['msu7Name'])
    jsonOutput <- fromJSON(rOutput)
    if (jsonOutput['rappredName'] == "None"){
        id <- jsonOutput['raprepName']
    }
    else if (jsonOutput['rapredName'] == "None") {
        id <- jsonOutput['rappredName']
    }
    else {
        id <- jsonOutput['raprepName']
    }
    
    locName <- jsonOutput['msu7Name']
    iricname <- jsonOutput['iricname']
    #print(iricname)
    
    if (id != "None") {
        return (list(id,locName,iricname))
    }
    
}

#' getIds
#'
#' This function is called for each locus and has to return the list of ids 
#' present in the locus
#' 
#' @param i number
#' @param locusList list
#' @return This function will return a list with all the ids from a locus
#' @importFrom jsonlite fromJSON
#' @importFrom findpython find_python_cmd
#' @rdname getIds-function
getIds <- function (i, locusList) {
    ##PATH for package when it will be installed -> when it will be released
    path <- system.file("python",
                        "run.py",
                        package = "rRice")
    
    ##manage the spaces -> for example "Program Files" under windows will 
    ##generate an error because with system2 we generate a command line
    ##with multiple arguments in one string. 
    if (Sys.info()["sysname"] == "Windows"){
        path <- shortPathName(path)
    }
    
    listIds <- data.frame()
    
    #path2Script = paste(c(path), collapse = '')
    
    ch = as.character(locusList[i,1])
    start = as.character(locusList[i,2])
    end = as.character(locusList[i,3])
    
    if (ch != "" && start != "" && end != "") {
        ##Call run.py from python
        if (Sys.info()["sysname"] == "Windows"){
            args = c(path, ch, start, end, "call_snpSeek", "None")
            cmd <- findpython::find_python_cmd()
            rOutput = system2(command = cmd, args=args, stdout = TRUE)
        }
        else {
            args = c(ch, start, end, "call_snpSeek", "None")
            rOutput = system2(command = path, args=args, stdout = TRUE)
        }
        
        
        #rOutput = system2(command=path, args=args, stdout=TRUE)
        
        lapply(1 : length(rOutput),
               function(x) returnError(rOutput[x]))
        
        rOutput <- lapply(1 : length(rOutput),
                          function(x) getOutPutJSON(rOutput[x]))
        
        rOutput[sapply(rOutput, is.null)] <- NULL
        
        ##print(rOutput)
        
        
        if (length(rOutput) > 0) {
            #print(rOutput)
            #jsonOutput <- fromJSON(rOutput[[1]])
            
            listIds <- lapply(1 : length(rOutput),
                              FUN = function(x) id(rOutput[[x]]))
        }
        
        ##Remove all the NULL object from the list
        listIds[sapply(listIds, is.null)] <- NULL
        
        ##remove double ids
        listIds <- lapply(1 : length(listIds),
                          FUN = function(x) noDoubleIds(listIds[[x]]))
        
        ##to get only one list !!
        liste <- list()
        lapply(1 : length(listIds),
               FUN = function(x){liste <<- append(liste,listIds[[x]])})
        
        ##print(liste)
        return (liste)
    }
    else {
        return (list())
    }
}

#' CallSnpSeek
#' 
#' It will return a list of IDs and msu7Name
#' 
#' @param locus the list of locus for which we want the ids
#' @return the list of id's of each genes we want
#' @export
#' @rdname callSnpSeek-function
#' @examples 
#' locusList <- data.frame(ch = c("1"),
#'                         st = c("148907"),
#'                         end = c("248907"))
#'                   
#' callSnpSeek(locusList)
callSnpSeek <- function(locus){
    
    listIds <- data.frame()
    
    if (length(locus) > 0) {
        ##We call the function creationGeneDB1 to create our newGene
        listIds <- lapply(1 : nrow(locus),
                          FUN = function(x) getIds(x, locus))
        
        
        ##Remove all the NULL object from the list
        listIds[sapply(listIds, is.null)] <- NULL
        
        ##To delete all the geneDB1 which exists in double
        listIds <- unique(listIds)
        
        ##print(listIds)
        return (listIds)
    }
    else {
        return (list())
    }
    
}