R/readPanels.R

In seqinr: Biological Sequences Retrieval and Analysis

readPanels <- function(file,
                       colnames = c("marker", "dye.col", "min.bp", "max.bp", "exp.pcg", "repeat.bp",
                                    "stutter.pc", "uknw", "allele names")){
    src <- readLines(file)
    iPanel <- which(substr(src, start = 1, stop = 6) == "Panel\t")
    
    infos <- src[1:(iPanel[1] - 1)]
    result <- list(infos = infos)
    
    starts <- iPanel + 1
    stops  <- c(iPanel[-1] - 1, length(src))
    
    for(i in seq_len(length(iPanel))){
        toimport <- src[starts[i]:stops[i]]
        # Change all runs of tabulations by a single one:
        toimport <- gsub("\t{2,}", "\t", toimport)
        mycon <- textConnection(toimport)
        result[[i+1]] <- utils::read.table(mycon, sep = "\t", quote = "")
        close(mycon)
        # remove empty columns
        # (I guess this is no more necessary now that runs of
        # tabulation are preprocessed)
        tokeep <- rep(TRUE, ncol(result[[i+1]]))
        for(j in 1:ncol(result[[i+1]])){
            if(all(is.na(result[[i+1]][,j]))){
                tokeep[j] <- FALSE
            }
        }
        result[[i+1]] <- result[[i+1]][, tokeep]
        # There must be 9 columns
        if(ncol(result[[i+1]]) != 9) stop("wrong column number")
        colnames(result[[i+1]]) <- colnames
        
        headeritems <- unlist(strsplit(src[iPanel[i]], split = "\t"))
        # remove empty elements
        if(any(nchar(headeritems) == 0)){
            headeritems <- headeritems[-which(nchar(headeritems) == 0)]
        }
        names(result)[i+1] <- headeritems[2]
    }
    return(result)
}