# Genepop -> FSTAT
#' @title Convert Genepop to FSTAT format.
#' @description Function to convert Genepop to FSTAT
#' @param genepop the genepop data to be manipulated. This can be either a file path
#' or a dataframe read in with tab separation, header=FALSE , quote="", and stringsAsFactors=FALSE.
#' This will be the standard genepop format with the first n+1 rows corresponding to the n loci names,
#' or a single comma delimited row of loci names followed by the locus data. Populations are
#' separated by "Pop". Each individual ID is linked to the locus data by " , " (space,space space) and is read in as
#' as a single row (character).
#' @param path the filepath and filename of output.
#' @param addworkspace logical statement defining whether the converted data
#' should be saved as a file specified in the path (default) argument or whether it should be returned to the workspace
#' if returned to the workspace the object will be called "Output_fstat".
#' @rdname genepop_fstat
#' @importFrom data.table fread
#' @importFrom utils write.table
#' @export
##
genepop_fstat <- function(genepop,path=NULL,addworkspace=FALSE)
{
#Check to see if genepop is a data.frame from the workspace and convert to data.table
if(is.data.frame(genepop)){genepop <- as.data.table(genepop)}
#Check to see if genepop is a file path or dataframe
if(is.character(genepop)){
genepop <- data.table::fread(genepop,
header = FALSE, sep = "\t",
stringsAsFactors = FALSE)
}
## check if loci names are read in as one large character vector (1 row)
header <- genepop[1,]
if(length(gregexpr(',', header, fixed=F)[[1]])>1){
lociheader <- strsplit(header,",")
lociheader <- gsub(" ","",unlist(lociheader))
#remove the first column of loci names
genepop <- as.vector(genepop)
genepop <- genepop[-1,]
genepop <- c(lociheader,genepop)
genepop <- as.data.table(genepop,stringsAsFactors = FALSE)
}
## Stacks version information
stacks.version <- genepop[1,] #this could be blank or any other source. First row is ignored by genepop
#Remove first label of the stacks version
genepop <- genepop[-1,]
colnames(genepop) <- "data"
#ID the rows which flag the Populations
Pops <- which(genepop$data == "Pop" | genepop$data =="pop" | genepop$data == "POP")
npops <- 1:length(Pops)
## separate the data into the column headers and the rest
ColumnData <- genepop$data[1:(Pops[1]-1)]
ColumnData <- gsub("\r","",ColumnData)#remove any hidden carriage returns
snpData <- genepop[Pops[1]:NROW(genepop),]
#Get a datafile with just the snp data no pops
tempPops <- which(snpData$data=="Pop"| snpData$data =="pop" | snpData$data == "POP") ## Changed because we allowed
snpData <- snpData[-tempPops,]
#separate the snpdata
temp <- as.data.frame(do.call(rbind, strsplit(snpData$data," ")))
#data format check
if(unique(temp[,2])!="," | !length(which(temp[,3]==""))>1){
stop("Genepop sampleID delimiter not in proper format. Ensure sampleIDs are separated from loci by ' , ' (space comma space space). Function stopped.",call. = FALSE)
}
temp2 <- temp[,4:length(temp)] #split characters by spaces
#Contingency to see if R read in the top line as the "stacks version"
if (length(temp2)!=length(ColumnData)){colnames(temp2) <- c(stacks.version,ColumnData)}
if (length(temp2)==length(ColumnData)){colnames(temp2) <- ColumnData}
if (length(temp2)!=length(ColumnData)){stacks.version="No STACKS version specified"}
#stacks version character
stacks.version <- as.character(stacks.version)
## Get the population names (prior to the _ in the Sample ID)
NamePops <- temp[,1] # Sample names of each
NameExtract <- substr(NamePops,1,regexpr("_",NamePops)-1)
#convert the snp data into character format to get rid of factor levels
temp2[] <- lapply(temp2, as.character)
#get the allele values for FSTAT summary header
firstAllele <- as.data.frame(sapply(temp2,function(x)as.numeric(as.character(substring(x,1,3)))))
secondAllele <- as.data.frame(sapply(temp2,function(x)as.numeric(as.character(substring(x,4,6)))))
## replace Genepop blanks ("000000") with fstat blanks ("0")
temp2[temp2=="000000"]=" 0"
## population column
numPop=rep(1:length(table(NameExtract)),
times=table(factor(NameExtract,levels=unique(NameExtract))))
## Add loci back together as one character vector
Loci <- do.call(paste,c(temp2[,], sep=" "))
## Add numeric population grouping and spacing
Loci <- paste(numPop,Loci,sep=" ") #separated by three spaces
## Add the loci names
Loci <- c(names(temp2),Loci)
## Add the header information
nPops <- length(unique(numPop))
nLoci <- length(temp2)
allelemax <- max(c(max(as.matrix(firstAllele)),max(as.matrix(secondAllele))))
allelecallsize <- nchar(temp2[1,1])/2
FStat_header <- paste(nPops,nLoci,allelemax,allelecallsize,sep=" ")
#compile into fstat format
Output <- c(FStat_header,Loci)
#return to the workspace
if(addworkspace){
Output_fstat <- as.data.frame(Output)
}
# Save the file
if(!addworkspace){
utils::write.table(Output,path,col.names=FALSE,row.names=FALSE,quote=FALSE)
}
} #End function
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