#'Load results of BLAST database search to R
#'
#'Loads BLAST search results in .txt format to R list structure.
#'
#'@param blastResultsFile .txt file containing results of BLAST database search obtained using the -outfmt 0 command.
#'@param results number of top results for each query sequence that will be loaded to R
#'
#'@return List containing top BLAST atabase matches for each query sequence.
#'
#'@examples
#'scoreList <- readBlastResults("BLAST_S1_fw_condensed.txt", results = 1000)
#'
#'@export
#'
readBlastResults <- function (blastResultsFile, results = 10)
{
bl <-read.delim(blastResultsFile)
outputPosition <- grep ("Query=", bl[[1]])
scoreMatrix <- matrix(rep(0, 3*results), nrow = results, ncol = 3)
colnames(scoreMatrix)<- c("Name", "BitScore", "Evalue")
scoreList <- replicate(length(outputPosition),scoreMatrix, simplify=FALSE)
for (i in 1:length(outputPosition)){
names(scoreList)[i]<-substr(bl[[1]][outputPosition[i]],8,nchar(as.character(bl[[1]][outputPosition[i]])))
for (j in 1:results){
radek <- strsplit(as.character(bl[[1]][j+outputPosition[i]+3]), " ")
radek<- radek[[1]][radek[[1]] != ""]
scoreList[[i]][j,1]<- paste(radek[1], radek[2])
scoreList[[i]][j,2]<- radek[3]
scoreList[[i]][j,3]<- radek[4]
}
}
return(scoreList)
}
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