def delimit_species(args):
if not os.path.exists(args.stree):
print("Input tree file does not exists: %s" % args.strees)
sys.exit()
try:
tree = args.stree
treetest = open(args.stree)
l1 = treetest.readline()
treetest.close()
inputformat = "nexus"
if l1.strip() == "#NEXUS":
inputformat = "nexus"
else:
inputformat = "raxml"
bsptp = bootstrap_ptp(filename=args.stree,
ftype=inputformat,
reroot=args.sreroot,
method=args.sstrategy,
firstktrees=args.num_trees)
if args.outgroups != None and len(args.outgroups) > 0:
bsptp.remove_outgroups(args.outgroups, remove=args.delete)
pars, settings = bsptp.delimit(args=args)
pp = partitionparser(taxa_order=bsptp.taxa_order,
partitions=pars,
scale=1)
pp.summary(fout=args.output, bnmi=args.nmi, sp_setting=settings)
if bsptp.numtrees > 1:
min_no_p, max_no_p, mean_no_p = pp.hpd_numpartitions()
print("Estimated number of species is between " + repr(min_no_p) +
" and " + repr(max_no_p))
print("Mean: " + repr(mean_no_p))
print_run_info(args=args)
except treeIO.newick.NewickError:
print("Unexisting tree file or Malformed newick tree structure.")
def delimit_species(args):
if not os.path.exists(args.stree):
print("Input tree file does not exists: %s" % args.strees)
sys.exit()
try:
tree = args.stree
treetest = open(args.stree)
l1 = treetest.readline()
treetest.close()
inputformat = "nexus"
if l1.strip() == "#NEXUS":
inputformat = "nexus"
else:
inputformat = "raxml"
bsptp = bootstrap_ptp(
filename=args.stree,
ftype=inputformat,
reroot=args.sreroot,
method=args.sstrategy,
firstktrees=args.num_trees,
)
if args.outgroups != None and len(args.outgroups) > 0:
bsptp.remove_outgroups(args.outgroups, remove=args.delete)
pars, settings = bsptp.delimit(args=args)
pp = partitionparser(taxa_order=bsptp.taxa_order, partitions=pars, scale=1)
pp.summary(fout=args.output, bnmi=args.nmi, sp_setting=settings)
if bsptp.numtrees > 1:
min_no_p, max_no_p, mean_no_p = pp.hpd_numpartitions()
print("Estimated number of species is between " + repr(min_no_p) + " and " + repr(max_no_p))
print("Mean: " + repr(mean_no_p))
print_run_info(args=args)
except treeIO.newick.NewickError:
print("Unexisting tree file or Malformed newick tree structure.")
inputformat = "nexus"
else:
inputformat = "raxml"
bsptp = bootstrap_ptp(filename=args.stree,
ftype=inputformat,
reroot=args.sreroot,
method=args.sstrategy,
firstktrees=args.num_trees)
if args.outgroups != None and len(args.outgroups) > 0:
bsptp.remove_outgroups(args.outgroups, remove=args.delete)
pars, settings = bsptp.delimit(args=args)
pp = partitionparser(taxa_order=bsptp.taxa_order,
partitions=pars,
scale=args.sscale)
pp.summary(fout=args.output, bnmi=args.nmi, sp_setting=settings)
if bsptp.numtrees > 1:
min_no_p, max_no_p, mean_no_p = pp.hpd_numpartitions()
print("Estimated number of species is between " + repr(min_no_p) +
" and " + repr(max_no_p))
print("Mean: " + repr(mean_no_p))
print_run_info(args=args)
except ete2.parser.newick.NewickError:
print("Unexisting tree file or Malformed newick tree structure.")
ftype=inputformat,
reroot=args.reroot,
method=args.method,
seed=args.seed,
thinning=args.imcmc,
sampling=args.nmcmc,
burnin=args.burnin,
firstktrees=args.num_trees,
)
if args.outgroups != None and len(args.outgroups) > 0:
bbptp.remove_outgroups(args.outgroups, remove=args.delete, output=args.trees + ".NoOutgroups")
pars, llhs, settings = bbptp.delimit()
pp = partitionparser(taxa_order=bbptp.taxa_order, partitions=pars, llhs=llhs, scale=args.scale)
if bbptp.numtrees == 1:
pp.summary(
fout=args.output,
bnmi=args.nmi,
ML_par=bbptp.get_maxhhl_partition(),
ml_spe_setting=bbptp.maxhhlsetting,
sp_setting=settings,
)
else:
pp.summary(fout=args.output, bnmi=args.nmi, sp_setting=settings)
min_no_p, max_no_p, mean_no_p = pp.hpd_numpartitions()
print("Estimated number of species is between " + repr(min_no_p) + " and " + repr(max_no_p))
print("Mean: " + "{0:.2f}".format(mean_no_p))
method=args.method,
seed=args.seed,
thinning=args.imcmc,
sampling=args.nmcmc,
burnin=args.burnin,
firstktrees=args.num_trees)
if args.outgroups != None and len(args.outgroups) > 0:
bbptp.remove_outgroups(args.outgroups,
remove=args.delete,
output=args.trees + ".NoOutgroups")
pars, llhs, settings = bbptp.delimit()
pp = partitionparser(taxa_order=bbptp.taxa_order,
partitions=pars,
llhs=llhs,
scale=args.scale)
if bbptp.numtrees == 1:
pp.summary(fout=args.output,
bnmi=args.nmi,
ML_par=bbptp.get_maxhhl_partition(),
ml_spe_setting=bbptp.maxhhlsetting,
sp_setting=settings)
else:
pp.summary(fout=args.output, bnmi=args.nmi, sp_setting=settings)
min_no_p, max_no_p, mean_no_p = pp.hpd_numpartitions()
print("Estimated number of species is between " + repr(min_no_p) +
" and " + repr(max_no_p))
print("Mean: " + "{0:.2f}".format(mean_no_p))
method=args.method,
seed=args.seed,
thinning=args.imcmc,
sampling=args.nmcmc,
burnin=args.burnin,
firstktrees=args.num_trees)
if args.outgroups != None and len(args.outgroups) > 0:
bbptp.remove_outgroups(args.outgroups,
remove=args.delete,
output=args.trees + ".NoOutgroups")
pars, llhs, settings = bbptp.delimit()
pp = partitionparser(taxa_order=bbptp.taxa_order,
partitions=pars,
llhs=llhs)
if bbptp.numtrees == 1:
pp.summary(fout=args.output,
bnmi=args.nmi,
ML_par=bbptp.get_maxhhl_partition(),
ml_spe_setting=bbptp.maxhhlsetting,
sp_setting=settings)
else:
pp.summary(fout=args.output, bnmi=args.nmi, sp_setting=settings)
min_no_p, max_no_p, mean_no_p = pp.hpd_numpartitions()
print("Estimated number of species is between " + repr(min_no_p) +
" and " + repr(max_no_p))
print("Mean: " + "{0:.2f}".format(mean_no_p))
treetest.close()
inputformat = "nexus"
if l1.strip() == "#NEXUS":
inputformat = "nexus"
else:
inputformat = "raxml"
bbptp = bayesianptp(filename = args.trees, ftype = inputformat,
reroot = args.reroot, method = args.method, seed = args.seed,
thinning = args.imcmc, sampling = args.nmcmc, burnin = args.burnin,
firstktrees = args.num_trees)
if args.outgroups!= None and len(args.outgroups) > 0:
bbptp.remove_outgroups(args.outgroups, remove = args.delete, output = args.trees + ".NoOutgroups")
pars, llhs, settings = bbptp.delimit()
pp = partitionparser(taxa_order = bbptp.taxa_order, partitions = pars, llhs = llhs)
if bbptp.numtrees == 1:
pp.summary(fout = args.output, bnmi = args.nmi, ML_par = bbptp.get_maxhhl_partition(),
ml_spe_setting = bbptp.maxhhlsetting, sp_setting = settings)
else:
pp.summary(fout = args.output, bnmi = args.nmi, sp_setting = settings)
min_no_p, max_no_p, mean_no_p = pp.hpd_numpartitions()
print("Estimated number of species is between " + repr(min_no_p) + " and " + repr(max_no_p))
print("Mean: " + "{0:.2f}".format(mean_no_p))
print("")
print_run_info(args, bbptp.numtrees)
def download1(self):
try:
self.toolButton_8.setEnabled(True)
self.toolButton_9.setEnabled(True)
m1 = int(self.m1.text())
m3 = int(self.m3.text())
m4 = float(self.m4.text())
m5 = int(self.m5.text())
m8 = int(self.m8.text())
m2 = self.m2.text()
m6 = self.m6.text()
def_dict.default_factory = partial(factory, m6)
m7 = def_dict[self.m7.text()]
m6 = def_dict[self.m6.text()]
tmpfname = self.filepath['path']
origfname = None
_, filename = os.path.split(tmpfname)
filename = filename.split(".")[0]
output = self.f.name
self.outpath['output'] = output
print(self.outpath['output'])
open_file = tmpfname
self.unique = str(int(time.time()))
save_file = output
with open(open_file) as treetest:
l1 = treetest.readline()
if self.radioButton.isChecked() == True:
inputformat = "nexus"
reroot = False
elif self.radioButton_2.isChecked() == True:
inputformat = "raxml"
reroot = False
elif self.radioButton_3.isChecked() == True:
inputformat = "raxml"
reroot = True
else:
inputformat = "raxml"
reroot = True
bsptp = bootstrap_ptp(filename=open_file,
ftype=inputformat,
reroot=reroot,
method=m2,
firstktrees=m8)
pars, settings = bsptp.delimit(spe_rate=-1.0,
max_iters=20000,
min_br=0.0001,
whiten=False,
strategy=m2,
sprint=False,
pvalue=0.001)
pp = partitionparser(taxa_order=bsptp.taxa_order,
partitions=pars,
scale=500,
fileextension=open_file,
ptp_status="ptp")
pp.summary(fout=os.path.join(save_file, f"PTP_{self.unique}"),
bnmi=False,
sp_setting=settings)
onlyfiles = [
self.listWidget.addItem(f) for f in os.listdir(save_file)
if os.path.isfile(os.path.join(save_file, f))
]
if bsptp.numtrees > 1:
min_no_p, max_no_p, mean_no_p = pp.hpd_numpartitions()
print("Estimated number of species is between " +
repr(min_no_p) + " and " + repr(max_no_p))
print("Mean: " + repr(mean_no_p))
except Exception as e:
QMessageBox.warning(
self, "Warning",
f"The species delimitation output is not obtained because {e}"
)
return
QMessageBox.information(
self, "Information",
"The species delimitation results generated successfully")
def download2(self):
try:
self.toolButton_8.setEnabled(True)
self.toolButton_9.setEnabled(True)
m1 = int(self.m1.text())
m3 = int(self.m3.text())
m4 = float(self.m4.text())
m5 = int(self.m5.text())
m8 = int(self.m8.text())
m2 = self.m2.text()
m6 = self.m6.text()
def_dict.default_factory = partial(factory, m6)
m7 = def_dict[self.m7.text()]
m6 = def_dict[self.m6.text()]
tmpfname = self.filepath['path']
origfname = None
_, filename = os.path.split(tmpfname)
filename = filename.split(".")[0]
output = self.f.name
self.outpath['output'] = output
print(self.outpath['output'])
open_file = tmpfname
self.unique = str(int(time.time()))
save_file = output
with open(open_file) as treetest:
l1 = treetest.readline()
if self.radioButton.isChecked() == True:
inputformat = "nexus"
reroot = False
elif self.radioButton_2.isChecked() == True:
inputformat = "raxml"
reroot = False
elif self.radioButton_3.isChecked() == True:
inputformat = "raxml"
reroot = True
else:
inputformat = "raxml"
reroot = True
bbptp = bayesianptp(filename=open_file,
ftype=inputformat,
reroot=reroot)
bbptp = bayesianptp(filename=open_file,
ftype=inputformat,
reroot=reroot,
method=m2,
seed=m5,
thinning=m3,
sampling=m1,
burnin=m4,
firstktrees=m8)
if m6 != None and len(m6) > 0:
bbptp.remove_outgroups(m6,
remove=m7,
output=open_file + ".NoOutgroups")
pars, llhs, settings = bbptp.delimit()
pp = partitionparser(taxa_order=bbptp.taxa_order,
partitions=pars,
llhs=llhs,
fileextension=open_file,
ptp_status="bptp")
if bbptp.numtrees == 1:
pp.summary(fout=os.path.join(save_file, f"bPTP_{self.unique}"),
ML_par=bbptp.get_maxhhl_partition(),
ml_spe_setting=bbptp.maxhhlsetting,
sp_setting=settings)
else:
pp.summary(fout=os.path.join(save_file,
f"bPTP_{int(time.time())}"),
sp_setting=settings)
min_no_p, max_no_p, mean_no_p = pp.hpd_numpartitions()
onlyfiles = [
self.listWidget.addItem(f) for f in os.listdir(save_file)
if os.path.isfile(os.path.join(save_file, f))
]
except Exception as e:
QMessageBox.warning(
self, "Warning",
f"The species delimitation output is not obtained because {e}"
)
return
QMessageBox.information(
self, "Information",
"The species delimitation results generated successfully")
l1 = treetest.readline()
treetest.close()
inputformat = "nexus"
if l1.strip() == "#NEXUS":
inputformat = "nexus"
else:
inputformat = "raxml"
bsptp = bootstrap_ptp(filename = args.stree, ftype = inputformat, reroot = args.sreroot, method = args.sstrategy, firstktrees = args.num_trees)
if args.outgroups!= None and len(args.outgroups) > 0:
bsptp.remove_outgroups(args.outgroups, remove = args.delete)
pars, settings = bsptp.delimit(args=args)
pp = partitionparser(taxa_order = bsptp.taxa_order, partitions = pars, scale = args.sscale)
pp.summary(fout = args.output, bnmi = args.nmi, sp_setting = settings)
if bsptp.numtrees > 1:
min_no_p, max_no_p, mean_no_p = pp.hpd_numpartitions()
print("Estimated number of species is between " + repr(min_no_p) + " and " + repr(max_no_p))
print("Mean: " + repr(mean_no_p))
print_run_info(args = args)
except ete2.parser.newick.NewickError:
print("Unexisting tree file or Malformed newick tree structure.")
