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 __init__(self, server, pw, name=None):
self.the_type = self.__class__.__name__
if name is None:
name = socket.gethostname()
self.name = name
self.server = server
self.pw = pw
self.logs = []
self.thrownlog = 0
self.last_sc_upload = time.time()
self.the_logger = logging.getLogger(self.name)
self.the_logger.setLevel(logging.INFO)
self.queues = []
self.overlord = self.make_lord('commands_%s_%s' % (self.the_type, self.name))
self.config = {}
config = self.get_config()
self.config_update(config)
self.config = config
self.stats = self.get_stats()
self.stats['started'] = time.mktime(time.gmtime())
logconf = self.config.get('logging', {})
logconf['filename'] = './%s_%s.log' % (self.the_type, self.name)
logging.basicConfig(**logconf)
self.the_logger = logging.getLogger(self.name)
self.the_logger.setLevel(self.config.get('loglevel', logging.INFO))
self.log('info', 'I live to serve!')
self.sched = Scheduler()
self.sched.start()
self.sched.add_interval_job(self.upload, seconds=self.config.get('check_interval', 60))
ComLine.__init__(self)
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)