def baseml(vers=None, verbose=False):
from Bio.Phylo.PAML import baseml
if vers is not None:
versions = [vers]
else:
versions = VERSIONS
tests = [
("model", list(range(0, 9))),
("nhomo", [1, 3, 4]),
("nparK", list(range(1, 5))),
("alpha1rho1", None),
("SE", None),
]
alignment = os.path.join("Alignments", "alignment.phylip")
tree = os.path.join("Trees", "species.tree")
for test in tests:
print(test[0])
bml = baseml.Baseml()
for version in versions:
print(f"\t{version.replace('_', '.')}")
if test[1] is not None:
for n in test[1]:
if (version in ["4_3", "4_4", "4_4c", "4_5"]
and test[0] == "nparK" and n in [3, 4]):
continue
print(f"\t\tn = {n}")
ctl_file = os.path.join("Control_files", "baseml",
f"{test[0]}{n}.ctl")
bml.read_ctl_file(ctl_file)
bml.alignment = alignment
bml.tree = tree
out_file = f"{test[0]}{n}-{version}.out"
bml.out_file = os.path.join("Results", "baseml", test[0],
out_file)
bin = f"baseml{version}"
bml.run(command=bin, verbose=verbose, parse=False)
else:
if version in ["4_3", "4_4", "4_4c", "4_5"
] and test[0] == "alpha1rho1":
continue
ctl_file = os.path.join("Control_files", "baseml",
f"{test[0]}.ctl")
bml.read_ctl_file(ctl_file)
bml.alignment = alignment
bml.tree = tree
out_file = f"{test[0]}-{version}.out"
bml.out_file = os.path.join("Results", "baseml", test[0],
out_file)
bin = f"baseml{version}"
bml.run(command=bin, verbose=verbose, parse=False)
def baseml(vers=None, verbose=False):
from Bio.Phylo.PAML import baseml
if vers is not None:
versions = [vers]
else:
versions = VERSIONS
tests = [("model", list(range(0, 9))), ("nhomo", [1, 3, 4]),
("nparK", list(range(1, 5))), ("alpha1rho1", None), ("SE", None)]
alignment = os.path.join("Alignments", "alignment.phylip")
tree = os.path.join("Trees", "species.tree")
for test in tests:
print(test[0])
bml = baseml.Baseml()
for version in versions:
print("\t{0}".format(version.replace("_", ".")))
if test[1] is not None:
for n in test[1]:
if (version in ["4_3", "4_4", "4_4c", "4_5"] and
test[0] == "nparK" and n in [3, 4]):
continue
print("\t\tn = {0}".format(n))
ctl_file = (os.path.join("Control_files", "baseml",
"{0}{1}.ctl".format(test[0], n)))
bml.read_ctl_file(ctl_file)
bml.alignment = alignment
bml.tree = tree
out_file = "{0}{1}-{2}.out".format(test[0], n, version)
bml.out_file = (os.path.join("Results", "baseml", test[0],
out_file))
bin = "baseml{0}".format(version)
bml.run(command=bin, verbose=verbose, parse=False)
else:
if (version in ["4_3", "4_4", "4_4c", "4_5"] and
test[0] == "alpha1rho1"):
continue
ctl_file = (os.path.join("Control_files", "baseml",
"{0}.ctl".format(test[0])))
bml.read_ctl_file(ctl_file)
bml.alignment = alignment
bml.tree = tree
out_file = "{0}-{1}.out".format(test[0], version)
bml.out_file = (os.path.join("Results", "baseml", test[0],
out_file))
bin = "baseml{0}".format(version)
bml.run(command=bin, verbose=verbose, parse=False)
def setUp(self):
self.bml = baseml.Baseml()
searcher = NNITreeSearcher(scorer)
constructor = ParsimonyTreeConstructor(searcher)
pars_tree = constructor.build_tree(alignment)
print(pars_tree)
print('\n')
from Bio import Phylo
Phylo.write(pars_tree, aln + ".newick", 'newick')
with open(aln, 'r') as original:
allLines = original.readlines()
allLines[0] = allLines[0].rstrip() + "I\n"
modifyFile = open(aln, 'w')
for i in allLines:
modifyFile.write(i)
modifyFile.close()
bml = baseml.Baseml()
bml.alignment = aln
bml.tree = aln + ".newick"
bml.out_file = out
bml.working_dir = work_dir
bml.set_options(runmode=2, model=6)
bml.run()
with open(out, 'r') as result:
lines = result.readlines()
print("Best tree found:")
print(lines[-1])
last = lines[-1]
newtree = open(out + ".newick", "w")
newtree.write(last)
newtree.close()
