def run_in_tmp(fs, nexus):
"""
@param fs: fieldstorage-like user options
@param nexus: the nexus object that defines the tree and alignment
@return: from_paml
"""
# create the control object
config = Paml.PamlConfig()
config.set_hky()
# create the baseml.ctl control file
ctl_string = config.to_ctl_string()
with open(Paml.baseml_ctl, 'wt') as fout:
print >> fout, ctl_string
# create the nexus object that defines the tree and alignment
nexus = Nexus.get_sample_nexus_object()
# create the baseml.newick tree file
with open(Paml.baseml_newick, 'wt') as fout:
print >> fout, nexus.tree.get_newick_string()
# create the baseml.phylip alignment file
s_phylip = Phylip.get_alignment_string_non_interleaved(nexus.alignment)
with open(Paml.baseml_phylip, 'wt') as fout:
print >> fout, s_phylip
# run PAML
args = [Config.baseml_exe_path, Paml.baseml_ctl]
from_paml, to_paml = popen2.popen4(args)
return from_paml
def run_hky(tree, alignment):
"""
@param tree: a tree object
@param alignment: an alignment object
@return: messages from the program but not the results
"""
# create the baseml.ctl control file
config = PamlConfig()
config.set_hky()
config.to_ctl_string()
with open(baseml_ctl, 'wt') as fout:
print >> fout, config.to_ctl_string()
# create the nexus object that defines the tree and alignment
nexus = Nexus.get_sample_nexus_object()
# create the baseml.newick tree file
with open(baseml_newick, 'wt') as fout:
print >> fout, nexus.tree.get_newick_string()
# create the baseml.phylip alignment file
phylip_string = Phylip.get_alignment_string_non_interleaved(
nexus.alignment)
with open(baseml_phylip, 'wt') as fout:
print >> fout, phylip_string
# change the current directory to the data directory
with Util.remember_cwd():
os.chdir(Config.data_path)
# run PAML
exe_path = Config.baseml_exe_path
ctl_path = baseml_ctl
#cmd = '%s %s > /dev/null' % (exe_path, ctl_path)
#os.system(cmd)
from_paml, to_paml = popen2.popen4([exe_path, ctl_path])
#p = subprocess.Popen([cmd, arg], stdin=subprocess.PIPE, stdout=subprocess.PIPE, close_fds=True)
# change back to the old directory
return from_paml.read()
def run_in_tmp(fs, nexus):
"""
@param fs: fieldstorage-like user options
@param nexus: the nexus object that defines the tree and alignment
@return: from_paml
"""
# create the control object
config = Paml.PamlConfig()
config.set_hky()
# create the baseml.ctl control file
ctl_string = config.to_ctl_string()
with open(Paml.baseml_ctl, 'wt') as fout:
print >> fout, ctl_string
# create the nexus object that defines the tree and alignment
nexus = Nexus.get_sample_nexus_object()
# create the baseml.newick tree file
with open(Paml.baseml_newick, 'wt') as fout:
print >> fout, nexus.tree.get_newick_string()
# create the baseml.phylip alignment file
s_phylip = Phylip.get_alignment_string_non_interleaved(nexus.alignment)
with open(Paml.baseml_phylip, 'wt') as fout:
print >> fout, s_phylip
# run PAML
args = [Config.baseml_exe_path, Paml.baseml_ctl]
from_paml, to_paml = popen2.popen4(args)
return from_paml
def run_hky(tree, alignment):
"""
@param tree: a tree object
@param alignment: an alignment object
@return: messages from the program but not the results
"""
# create the baseml.ctl control file
config = PamlConfig()
config.set_hky()
config.to_ctl_string()
with open(baseml_ctl, "wt") as fout:
print >> fout, config.to_ctl_string()
# create the nexus object that defines the tree and alignment
nexus = Nexus.get_sample_nexus_object()
# create the baseml.newick tree file
with open(baseml_newick, "wt") as fout:
print >> fout, nexus.tree.get_newick_string()
# create the baseml.phylip alignment file
phylip_string = Phylip.get_alignment_string_non_interleaved(nexus.alignment)
with open(baseml_phylip, "wt") as fout:
print >> fout, phylip_string
# change the current directory to the data directory
with Util.remember_cwd():
os.chdir(Config.data_path)
# run PAML
exe_path = Config.baseml_exe_path
ctl_path = baseml_ctl
# cmd = '%s %s > /dev/null' % (exe_path, ctl_path)
# os.system(cmd)
from_paml, to_paml = popen2.popen4([exe_path, ctl_path])
# p = subprocess.Popen([cmd, arg], stdin=subprocess.PIPE, stdout=subprocess.PIPE, close_fds=True)
# change back to the old directory
return from_paml.read()
