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#' Read in uc files
#'
#' The read.uc function is used to read the output of clustering analyses from a UC file. The function stores the information in two tables: one for hit records (H) and one for cluster records (C).
#'
#' @usage read.uc(file)
#' @param file the name of the UC file that contains the clustering analysis results. The file should be specified with its full name, including the extension (e.g., all.minicircles.circ.id70.uc).
#' @return
#' \item{hits}{a table containing all the hit records from the UC file. Each row of the table represents a hit record, providing information about the alignment between a query sequence and a target sequence.}
#' \item{clusters}{a table containing all the cluster records from the UC file. Each row of the table represents a cluster record, providing information about the clustering of sequences into clusters.}
#' \item{clustnumbers}{a vector containing the cluster numbers (0-based). Each element of the vector represents a cluster identified in the clustering analysis.}
#' @importFrom utils read.table
#' @export
read.uc <- function(file) {
uc <- utils::read.table(file)
uc_C <- uc[which(uc$V1=='C'),]
rownames(uc_C) <- c(1:nrow(uc_C))
uc_C2 <- uc_C[,2]
uc_H <- uc[which(uc$V1 =='H'),]
if (nrow(uc_H) != 0) {
rownames(uc_H) <- c(1:nrow(uc_H))
}
return(list("hits" = uc_H, "clusters" = uc_C, "clustnumbers" = uc_C2))
}
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