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import os.path
import sys
VERSIONS = ["4_1", "4_3", "4_4", "4_4c", "4_5"]
VERBOSE = True
def codeml():
from Bio.Phylo.PAML import codeml
tests = [("aa_model0", "aa_alignment.phylip", "species.tree"),
("aa_pairwise", "aa_alignment.phylip", "species.tree"),
("all_NSsites", "alignment.phylip", "species.tree"),
("branchsiteA", "alignment.phylip", "species.tree"),
("clademodelC", "alignment.phylip", "species.tree"),
("freeratio", "alignment.phylip", "species.tree"),
("ngene2_mgene012", "lysinYangSwanson2002.nuc", "lysin.trees"),
("ngene2_mgene34", "lysinYangSwanson2002.nuc", "lysin.trees"),
("pairwise", "alignment.phylip", "species.tree"),
("SE", "alignment.phylip", "species.tree")]
for test in tests:
print test[0]
cml = codeml.Codeml()
cml.working_dir = "temp"
ctl_file = os.path.join("Control_files",
"codeml",
'.'.join([test[0], "ctl"]))
alignment = os.path.join("Alignments", test[1])
tree = os.path.join("Trees", test[2])
cml.read_ctl_file(ctl_file)
cml.alignment = alignment
cml.tree = tree
for version in VERSIONS:
print "\t{0}".format(version.replace('_', '.'))
out_file = '.'.join(['-'.join([test[0], version]), "out"])
cml.out_file = os.path.join("Results", "codeml", test[0], out_file)
bin = ''.join(["codeml", version])
cml.run(command=bin, verbose=VERBOSE)
def baseml():
from Bio.Phylo.PAML import baseml
tests = [("model", range(0, 9)), ("nhomo", [1, 3, 4]),
("nparK", 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)
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)
def yn00():
from Bio.Phylo.PAML import yn00
tests = ["yn00"]
alignment = os.path.join("Alignments", "alignment.phylip")
for test in tests:
print test[0]
yn = yn00.Yn00()
for version in VERSIONS:
print "\t{0}".format(version.replace('_', '.'))
ctl_file = os.path.join("Control_files", "yn00",
"{0}.ctl".format(test))
yn.read_ctl_file(ctl_file)
yn.alignment = alignment
out_file = "{0}-{1}.out".format(test, version)
yn.out_file = os.path.join("Results", "yn00", out_file)
bin = "yn00{0}".format(version)
yn.run(command=bin, verbose=VERBOSE)
if __name__ == "__main__":
if len(sys.argv) < 2:
sys.exit("specify a paml program")
if sys.argv[1] == "codeml":
codeml()
elif sys.argv[1] == "baseml":
baseml()
elif sys.argv[1] == "yn00":
yn00()
else:
sys.exit("specify a paml program")
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