def link_to_evol_model(self, path, model):
'''
link EvolTree to evolutionary model
* free-branch model ('fb') will append evol values to tree
* Site models (M0, M1, M2, M7, M8) will give evol values by site
and likelihood
:argument path: path to outfile containing model computation result
:argument model: either the name of a model, or a Model object (usually empty)
'''
if type(model) == str :
model = Model(model, self, path)
else:
model._load(path)
# new entry in _models dict
while model.name in self._models:
model.name = model.name.split('__')[0] + str(
(int(model.name.split('__')[1])
+1) if '__' in model.name else 0)
self._models[model.name] = model
if not os.path.isfile(path):
warn("ERROR: not a file: " + path)
return 1
if len(self._models) == 1 and model.properties['exec']=='codeml':
self.change_dist_to_evol('bL', model, fill=True)
def link_to_evol_model(self, path, model):
'''
link EvolTree to evolutionary model
* free-branch model ('fb') will append evol values to tree
* Site models (M0, M1, M2, M7, M8) will give evol values by site
and likelihood
:argument path: path to outfile containing model computation result
:argument model: either the name of a model, or a Model object (usually empty)
'''
if type(model) == str:
model = Model(model, self, path)
else:
model._load(path)
# new entry in _models dict
while model.name in self._models:
model.name = model.name.split('__')[0] + str(
(int(model.name.split('__')[1]) +
1) if '__' in model.name else 0)
self._models[model.name] = model
if not os.path.isfile(path):
warn("ERROR: not a file: " + path)
return 1
if len(self._models) == 1 and model.properties['exec'] == 'codeml':
self.change_dist_to_evol('bL', model, fill=True)
def run_model(self, model_name, ctrl_string='', keep=True, **kwargs):
'''
To compute evolutionnary models. e.g.: b_free_lala.vs.lele, will launch one free branch model, and store
it in "WORK_DIR/b_free_lala.vs.lele" directory
WARNING: this functionality needs to create a working directory in "rep"
WARNING: you need to have codeml and/or SLR in your path
The models available are:
=========== ============================= ==================
Model name Description Model kind
=========== ============================= ==================\n%s
=========== ============================= ==================\n
:argument model_name: a string like "model-name[.some-secondary-name]" (e.g.: "fb.my_first_try", or just "fb")
* model-name is compulsory, is the name of the model (see table above for the full list)
* the second part is accessory, it is to avoid over-writing models with the same name.
:argument ctrl_string: list of parameters that can be used as control file.
:argument kwargs: extra parameters should be one of: %s.
'''
from subprocess import Popen, PIPE
model_obj = Model(model_name, self, **kwargs)
fullpath = os.path.join (self.workdir, model_obj.name)
os.system("mkdir -p %s" %fullpath)
# write tree file
self.__write_algn(fullpath + '/algn')
if model_obj.properties['exec'] == 'Slr':
self.write(outfile=fullpath+'/tree',
format = (11))
else:
self.write(outfile=fullpath+'/tree',
format = (10 if model_obj.properties['allow_mark'] else 9))
# write algn file
## MODEL MODEL MDE
if ctrl_string == '':
ctrl_string = model_obj.get_ctrl_string(fullpath+'/tmp.ctl')
else:
open(fullpath+'/tmp.ctl', 'w').write(ctrl_string)
hlddir = os.getcwd()
os.chdir(fullpath)
bin = os.path.join(self.execpath, model_obj.properties['exec'])
try:
proc = Popen([bin, 'tmp.ctl'], stdout=PIPE)
except OSError:
raise Exception(('ERROR: {} not installed, ' +
'or wrong path to binary\n').format(bin))
run, err = proc.communicate()
if err is not None:
warn("ERROR: codeml not found!!!\n" +
" define your variable EvolTree.execpath")
return 1
if 'error' in run or 'Error' in run:
warn("ERROR: inside codeml!!\n" + run)
return 1
os.chdir(hlddir)
if keep:
setattr(model_obj, 'run', run)
self.link_to_evol_model(os.path.join(fullpath,'out'), model_obj)
def run_model(self, model_name, ctrl_string='', keep=True, **kwargs):
'''
To compute evolutionnary models. e.g.: b_free_lala.vs.lele, will launch one free branch model, and store
it in "WORK_DIR/b_free_lala.vs.lele" directory
WARNING: this functionality needs to create a working directory in "rep"
WARNING: you need to have codeml and/or SLR in your path
The models available are:
=========== ============================= ==================
Model name Description Model kind
=========== ============================= ==================\n%s
=========== ============================= ==================\n
:argument model_name: a string like "model-name[.some-secondary-name]" (e.g.: "fb.my_first_try", or just "fb")
* model-name is compulsory, is the name of the model (see table above for the full list)
* the second part is accessory, it is to avoid over-writing models with the same name.
:argument ctrl_string: list of parameters that can be used as control file.
:argument kwargs: extra parameters should be one of: %s.
'''
from subprocess import Popen, PIPE
model_obj = Model(model_name, self, **kwargs)
fullpath = os.path.join(self.workdir, model_obj.name)
os.system("mkdir -p %s" % fullpath)
# write tree file
self.__write_algn(fullpath + '/algn')
if model_obj.properties['exec'] == 'Slr':
self.write(outfile=fullpath + '/tree', format=(11))
else:
self.write(
outfile=fullpath + '/tree',
format=(10 if model_obj.properties['allow_mark'] else 9))
# write algn file
## MODEL MODEL MDE
if ctrl_string == '':
ctrl_string = model_obj.get_ctrl_string(fullpath + '/tmp.ctl')
else:
open(fullpath + '/tmp.ctl', 'w').write(ctrl_string)
hlddir = os.getcwd()
os.chdir(fullpath)
bin = os.path.join(self.execpath, model_obj.properties['exec'])
try:
proc = Popen([bin, 'tmp.ctl'], stdout=PIPE)
except OSError:
raise Exception(('ERROR: {} not installed, ' +
'or wrong path to binary\n').format(bin))
run, err = proc.communicate()
if err is not None:
warn("ERROR: codeml not found!!!\n" +
" define your variable EvolTree.execpath")
return 1
if 'error' in run or 'Error' in run:
warn("ERROR: inside codeml!!\n" + run)
return 1
os.chdir(hlddir)
if keep:
setattr(model_obj, 'run', run)
self.link_to_evol_model(os.path.join(fullpath, 'out'), model_obj)