genomics: Genomics related functions.

#' Import a GFF file
#' 
#' from: \url{http://genome.ucsc.edu/FAQ/FAQformat#format3}\cr
#' GFF (General Feature Format) lines are based on the GFF standard file
#' format.
#' GFF lines have nine required fields that must be tab-separated.
#' If the fields are separated by spaces instead of tabs, the track
#' will not display correctly. For more information on GFF format,
#' refer to \url{http://www.sanger.ac.uk/Software/formats/GFF}.
#' Here is a brief description of the GFF fields:\cr
#' seqname - The name of the sequence. Must be a chromosome or scaffold.\cr
#' source - The program that generated this feature.\cr
#' feature - The name of this type of feature. Some examples of standard\cr
#' feature types are "CDS", "start_codon", "stop_codon", and "exon".\cr
#' start - The starting position of the feature in the sequence. The first base
#' is numbered 1.\cr
#' end - The ending position of the feature (inclusive).\cr
#' score - A score between 0 and 1000. If the track line useScore attribute is
#' set to 1
#' for this annotation data set, the score value will determine the level of
#' gray
#' in which this feature is displayed (higher numbers = darker gray).
#' If there is no score value, enter ".".\cr
#' strand - Valid entries include '+', '-', or '.' (for don't know/don't care).\cr
#' frame - If the feature is a coding exon, frame should be a number between
#' 0-2 that
#' represents the reading frame of the first base. If the feature is not a
#' coding exon, the value should be '.'.\cr
#' group - All lines with the same group are linked together into a single
#' item.\cr
#' 
#' @param file the path to a gff file
#' @param row.pattern currently unused
#' @return a \code{data.frame} with these columns:  
#' "chr", "source", "feature", "start", "end", "score", "strand", "frame", "group"
#' @author Mark Cowley, 2/1/08
#' @export
import.gff <- function(file, row.pattern=NULL) {
    header <- readLines(file, 30)
    skip <- max( grep("^#", header) )
    res <- read.delim(file, skip=skip, header=FALSE)
    colnames(res) <- c("chr", "source", "feature", "start", "end", "score", "strand", "frame", "group")
    return( res )
}