Exemple #1
0
def main():
	input = ComLine(sys.argv[1:])
	vcf_file = VCF(input.args.vcf, input.args.thin, input.args.maf, input.args.indcov, input.args.snpcov, input.args.bi)
	#if input.args.filter == True:
	#	vcf_file.convert_filter()
	#else:

	#convert to Plink
	vcf_file.convert()

	populations = Popmap(input.args.popmap)
	vcf_file.plink()
	vcf_file.print_populations(populations)
	admix_run = Admixture(vcf_file.prefix, input.args.np, input.args.minK, input.args.maxK, input.args.rep, input.args.cv)
	admix_run.admix()
	admix_run.create_zip()
	admix_run.loglik()
	admix_run.print_cv()
Exemple #2
0
def main():
    input = ComLine(sys.argv[1:])

    vcf_file = VCF(input.args.vcf, input.args.thin, input.args.maf,
                   input.args.mac, input.args.indcov, input.args.snpcov,
                   input.args.bi, input.args.remove)

    #convert to Plink
    populations = Popmap(input.args.popmap)
    vcf_file.compIndLists(populations)
    vcf_file.convert()
    vcf_file.plink()
    vcf_file.print_populations(populations)
    vcf_file.print_individuals(populations)

    admix_run = Admixture(vcf_file.prefix, input.args.np, input.args.minK,
                          input.args.maxK, input.args.rep, input.args.cv)
    admix_run.admix()
    admix_run.create_zip()
    admix_run.loglik()
    admix_run.print_cv()