comparison multilocus_genotype.R @ 2:86aaadf36a4f draft

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1:ba2df0561b12

suppressPackageStartupMessages(library("ape"))
suppressPackageStartupMessages(library("ggplot2"))
suppressPackageStartupMessages(library("knitr"))

option_list <- list(
    make_option(c("--input_vcf"), action="store", dest="input_vcf", help="VCF input file")
    make_option(c("--input_pop_info"), action="store", dest="input_pop_info", help="Population information input file")
)

parser <- OptionParser(usage="%prog [options] file", option_list=option_list);
args <- parse_args(parser, positional_arguments=TRUE);

provesti_distance <- function(distance, selection) {
  eval(parse(text=paste("as.matrix(distance)[", selection, "]")));
}

#Read in VCF input file.
vcf <- read.vcfR(opts$input_vcf);

# Convert VCF file into formats compatiable with the Poppr package.
gind <- vcfR2genind(vcf);
# Add population information to the genind object.
poptab <- read.table(opt$input_pop_info, check.names=FALSE, header=T, na.strings = c("", "NA"));

2:86aaadf36a4f

suppressPackageStartupMessages(library("ape"))
suppressPackageStartupMessages(library("ggplot2"))
suppressPackageStartupMessages(library("knitr"))

option_list <- list(
    make_option(c("--input_vcf"), action="store", dest="input_vcf", help="VCF input file"),
    make_option(c("--input_pop_info"), action="store", dest="input_pop_info", help="Population information input file")
)

parser <- OptionParser(usage="%prog [options] file", option_list=option_list);
args <- parse_args(parser, positional_arguments=TRUE);

provesti_distance <- function(distance, selection) {
  eval(parse(text=paste("as.matrix(distance)[", selection, "]")));
}

#Read in VCF input file.
vcf <- read.vcfR(opt$input_vcf);

# Convert VCF file into formats compatiable with the Poppr package.
gind <- vcfR2genind(vcf);
# Add population information to the genind object.
poptab <- read.table(opt$input_pop_info, check.names=FALSE, header=T, na.strings = c("", "NA"));