def main(): input = ComLine(sys.argv[1:]) executable = "BA3-SNPS" if cmd_exists(executable) is False: if cmd_exists("ba3-snps") is True: executable = "ba3-snps" else: print("BA3-SNPS is not installed.") print("Please install BA3-SNPS before proceeding.") raise SystemExit ba = Bayesass(executable, input.args.immanc, input.args.loci, input.args.out, input.args.generations, input.args.burnin, input.args.seed) for i in range(1, input.args.reps + 1, 1): print("Running repetition", i, "of", input.args.reps) command = ba.create_command() stdout = ba.run_program(command, i) tune = Autotune(stdout, ba.m, ba.a, ba.f) tune.read_stdout() ba.m, ba.a, ba.f, mbool, abool, fbool = tune.determine_params( ba.testedM, ba.testedA, ba.testedF, ba.m, ba.a, ba.f) if all((mbool, abool, fbool)): earlyMessage = "Tuning completed early after " + str( i) + " rounds." ba.write_final_params(earlyMessage) raise SystemExit lateMessage = "Tuning not completed after " + str( input.args.reps) + " rounds." ba.write_final_params(lateMessage)
def main(): input = ComLine(sys.argv[1:]) cvFile = CV(input.args.cv) cvFile.readText() #cvFile.printText() so = CVStats(cvFile.d, input.args.out) so.calcStats() so.printStats() plot = Graphics(cvFile.d, input.args.cv) plot.printFigure()
def main(): input = ComLine(sys.argv[1:]) #handle bayescan output bs = BayeScan(input.args.bayescan, input.args.fdr) bsCommand = bs.build_command() bs.run_program(bsCommand) print(input.args.bayescan) #handle lositan output los = Lositan(input.args.lositan, 0.025) los.readLositan() los.printSignificant() #compare outputs com = Compare("bayescan.outliers.txt", "lositan.positive_selection.txt") com.readInput() com.printResults(input.args.vcf)
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()
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()
def main(): input = ComLine(sys.argv[1:]) verts = FindVertices(input.args.points, input.args.streams, input.args.code) print verts.vertices print verts.splits lines = FindLines(verts.vertices, verts.splits, input.args.code) exNodes = ExportTable(verts.vertices, "nodes.txt") exNodes.export(input.args.code) exBranches = ExportTable(verts.splits, "branches.txt") exBranches.export(input.args.code) #project the files into UTM Zone 12N - files must be in projected coordinate system for calculating stream length #need to add a command line option for changing the projection projection = "NAD 1983 UTM Zone 12N" prStreams = ProjectFile(verts.splits, projection) proj_streams = prStreams.define_projection() prSites = ProjectFile(input.args.points, projection) proj_sites = prSites.define_projection() #calculate stream distance dist_streams = CalculateDistance(proj_streams) dist_streams.calcdist()
def main(): input = ComLine(sys.argv[1:]) phy = Phylip(input.args.phy) pops = Popmap(input.args.popmap) VCF(phy, pops, input.args.out)
def main(): input = ComLine(sys.argv[1:]) pops = Popmap(input.args.popmap) vcf = VCF(input.args.vcf, pops) vcf.printFile(input.args.out) vcf.printPrivate(input.args.out)