61 lines
1.7 KiB
R
61 lines
1.7 KiB
R
#' @title Read GenePop Data
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#' @description Reads GenePop-formatted data
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#' @param tiedostonNimi Name of the file
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#' @return list containing data and popnames
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#' @export
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lueGenePopData <- function(tiedostonNimi) {
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fid <- readLines(tiedostonNimi)
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line <- fid[1] # ensimmäinen rivi
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line <- fid[2] # toinen rivi
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count <- rivinSisaltamienMjonojenLkm(line)
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line <- fid[3]
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lokusRiveja <- 1
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while (testaaPop(line) == 0) {
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lokusRiveja <- lokusRiveja + 1 # locus row
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line <- fid[2 + lokusRiveja]
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}
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if (lokusRiveja > 1) {
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nloci <- lokusRiveja
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} else {
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nloci <- count
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}
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popnames <- cell(10, 2)
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data <- zeros(100, nloci + 1)
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nimienLkm <- 0
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ninds <- 0
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poimiNimi <- 1
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digitFormat <- -1
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while (lokusRiveja < length(fid) - 2) {
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lokusRiveja <- lokusRiveja + 1 # Keeps the loop moving along
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line <- fid[lokusRiveja + 2]
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if (poimiNimi == 1) {
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# Edellinen rivi oli 'pop' (previous line was pop)
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nimienLkm <- nimienLkm + 1
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ninds <- ninds + 1
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if (nimienLkm > size(popnames, 1)) {
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popnames <- rbind(popnames, cell(10, 2))
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}
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nimi <- lueNimi(line)
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if (digitFormat == -1) {
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digitFormat <- selvitaDigitFormat(line)
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divider <- 10^digitFormat
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}
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popnames[nimienLkm, 1] <- nimi # N<>in se on greedyMix:iss<73>kin?!?
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popnames[nimienLkm, 2] <- ninds
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poimiNimi <- 0
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data <- addAlleles(data, ninds, line, divider)
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} else if (testaaPop(line)) {
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poimiNimi <- 1
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} else if (!is.na(line)) {
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ninds <- ninds + 1
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data <- addAlleles(data, ninds, line, divider)
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}
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}
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data <- data[1:(ninds * 2), ]
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popnames <- popnames[seq_len(nimienLkm), ]
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return(list(data = data, popnames = popnames))
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}
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