R/hdf_functions.R

In HiCBricks: Framework for Storing and Accessing Hi-C Data Through HDF Files

ReturnH5FileConnection <- function(File = NULL){
        HDF.File <- File
        if(Sys.getenv("HDF5_USE_FILE_LOCKING") == ""){
            Sys.setenv(HDF5_USE_FILE_LOCKING="FALSE")
        }
        HDF.Connection = H5Fopen(name=HDF.File)
        return(HDF.Connection)
}
ReturnH5Handler <- function(Path=NULL,File = NULL){
        Temp.connection <- ReturnH5FileConnection(File=File)
        Handle <- Temp.connection&Path
        return(Handle)
}
ReturnH5Attribute <- function(Handle = NULL, name = NULL, type = NULL){
    if(!H5Aexists(Handle, name)){
        CloseH5Con(Handle = Handle, type = type)
        stop("Attribute ",name," not found in HDF file.\n")
    }
    Attributes <- H5Aread(H5Aopen(Handle,name))
    return(Attributes)
}
CloseH5Con <- function(Handle = NULL, type = NULL){
    if(type == "group"){
        H5Gclose(Handle)
    }else if(type == "dataset"){
        H5Dclose(Handle)
    }else if(type == "file"){
        H5Fclose(Handle)
    }
}
Create_Path <- function(groups){
    Path.to.file <- ""
    for (x in groups) {
        Path.to.file <- file.path(Path.to.file,x)
    }
    # cat(Path.to.file,"\n")
    return(Path.to.file)
}
CreateGroups <- function(Group.path = NULL, File = NULL){
    Temp.connection = ReturnH5FileConnection(File=File)
    h5createGroup(file = Temp.connection, group = Group.path)
    H5Fclose(Temp.connection)
}
CreateDataset <- function(Path = NULL, File = NULL, name = NULL, dims = NULL, 
    maxdims = NULL, data_type = "H5T_NATIVE_DOUBLE", chunk_size = NULL, 
    compression_level = 6, fill_with = 0){
    Full.path <- Create_Path(Path)
    if(is.null(chunk_size)){
        chunk_size <- ceiling(dims/100)
    }
    H5Handler <- ReturnH5Handler(Path=Full.path,File = File)
    h5createDataset(file=H5Handler, dataset=name, dims= dims,
        maxdims = dims, H5type=data_type, chunk = chunk_size,
        level = compression_level, fillValue = fill_with)
    H5Gclose(H5Handler)
}
CreateAttributes <- function(Path = NULL, File = NULL, Attributes = NULL, 
    data_types = NULL, on = "group",
    dims = 1, maxdims = 1){
    if(is.null(Attributes) | is.null(data_types)){
        stop("Attributes and data_type cannot take NULL values")
    }
    Brick.handler <- ReturnH5Handler(Path = Path,File = File)
    for (i in seq_len(length(Attributes))) {
        An.attribute <- Attributes[i]
        data_type <- data_types[i]
        dim <- ifelse(!is.null(dims),dims[[i]],NULL)
        maxdim <- ifelse(!is.null(maxdims),maxdims[[i]],dim)
        MaxLen <- NULL
        if(data_type == "character"){
            ## If you can write a 280 char tweet, you can constrain 
            ## yourself to 280 chars here as well.
            ## It's not too small, its actually larger than the 
            ## linux filename limit.
            MaxLen <- 280
        }
        h5createAttribute(obj = Brick.handler, attr = An.attribute, 
            storage.mode = data_type, dims = dim, maxdims = maxdim, 
            size = MaxLen)
    }
    CloseH5Con(Handle = Brick.handler, type = on)
}
WriteAttributes <- function(Path = NULL, File = NULL, Attributes = NULL, 
    values = NULL, on = "group"){
    if(length(Attributes) != length(values)){
        stop("length of Attributes and value does not match")
    }
    Brick.handler <- ReturnH5Handler(Path = Path,File = File)
    for (i in seq_len(length(Attributes))) {
        value <- values[i]
        An.attribute <- Attributes[i]
        h5writeAttribute(attr = value, h5obj = Brick.handler, 
            name = An.attribute)
    }
    CloseH5Con(Handle = Brick.handler, type = on)
}
GetAttributes <- function(Path = NULL, File = NULL, Attributes = NULL, 
    on = "group", ignore.fun.cast = FALSE){
    Reference.object <- GenomicMatrix$new()
    FUNCasts <- Reference.object$matrices.chrom.attributes.fun.cast
    if(is.null(Path)){
        Brick.handler <- ReturnH5FileConnection(File = File)
    }else{
        Brick.handler <- ReturnH5Handler(Path = Path,File = File)
    }
    Attribute.df <- do.call(cbind,lapply(Attributes, function(An.attribute){
            Attr.val <- ReturnH5Attribute(Handle = Brick.handler, 
                name = An.attribute, type = on)
            if(!ignore.fun.cast){
                Val <- FUNCasts(type = An.attribute)(Attr.val)
            }else{
                Val <- Attr.val
            }
            temp.df <- data.frame(attribute = Val)
            colnames(temp.df) <- An.attribute 
            temp.df
        }))
    CloseH5Con(Handle = Brick.handler, type = on)
    return(Attribute.df)
}

# # InsertIntoDataset = function(Path = NULL, File = NULL, Name = NULL,
#  Data=NULL, Index = NULL,
# #     Start = NULL, Stride = NULL, Count = NULL){
# #     DatasetHandler <- ._Brick_Get_Something_(Group.path = Path, 
#       Brick = File, 
#  Name = Name, return.what = "group_handle")
# #     if(!is.null(Index)){
# #         h5writeDataset(obj=Data, h5loc=DatasetHandler, name=Chrom, 
# index=Index)
# #     }else if(!is.null(Count) & !is.null(Stride) & !is.null(Start)){
# #         h5writeDataset(obj=Data, h5loc=DatasetHandler, name=Chrom, 
# start=Start, stride=Stride, count=Count)
# #     }else{
# #         stop("FetchFromDataset expects one of Start, Stride, 
# Count if Index is NULL")
# #     }
# #     private$Flush.HDF()
# }