programs = ["codeml", "baseml", "yn00"]
prog = None
verbose = False
vers = None
if len(sys.argv) < 2:
print_usage()
for arg in sys.argv[1:]:
if arg == "-v":
verbose = True
elif arg in programs:
if prog is not None:
print("Only one program at a time, please.")
print_usage()
prog = arg
elif arg.replace(".", "_") in VERSIONS:
if vers is not None:
print("Only one version at a time, sorry.")
vers = arg.replace(".", "_")
else:
print("Unrecognized argument")
print_usage()
if prog is None:
print("No program specified")
print_usage()
if prog == "codeml":
codeml(vers, verbose)
elif prog == "baseml":
baseml(vers, verbose)
elif prog == "yn00":
yn00(vers, verbose)
programs = ["codeml", "baseml", "yn00"]
prog = None
verbose = False
vers = None
if len(sys.argv) < 2:
print_usage()
for arg in sys.argv[1:]:
if arg == "-v":
verbose = True
elif arg in programs:
if prog is not None:
print("Only one program at a time, please.")
print_usage()
prog = arg
elif arg.replace(".", "_") in VERSIONS:
if vers is not None:
print("Only one version at a time, sorry.")
vers = arg.replace(".", "_")
else:
print("Unrecognized argument")
print_usage()
if prog is None:
print("No program specified")
print_usage()
if prog == "codeml":
codeml(vers, verbose)
elif prog == "baseml":
baseml(vers, verbose)
elif prog == "yn00":
yn00(vers, 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")
