def assure_tree(params, tmp_dir='treetime_tmp'):
"""
Function that attempts to load a tree and build it from the alignment
if no tree is provided.
"""
if params.tree is None:
params.tree = os.path.basename(params.aln)+'.nwk'
print("No tree given: inferring tree")
utils.tree_inference(params.aln, params.tree, tmp_dir = tmp_dir)
if os.path.isdir(tmp_dir):
shutil.rmtree(tmp_dir)
try:
tt = TreeAnc(params.tree)
except:
print("Tree loading/building failed.")
return 1
return 0
def assure_tree(params, tmp_dir='treetime_tmp'):
"""
Function that attempts to load a tree and build it from the alignment
if no tree is provided.
"""
if params.tree is None:
params.tree = os.path.basename(params.aln)+'.nwk'
print("No tree given: inferring tree")
utils.tree_inference(params.aln, params.tree, tmp_dir = tmp_dir)
if os.path.isdir(tmp_dir):
shutil.rmtree(tmp_dir)
try:
tt = TreeAnc(params.tree)
except:
print("Tree loading/building failed.")
return 1
return 0
help='number of mutations/nodes that are printed to screen')
parser.add_argument('--verbose',
default=1,
type=int,
help='verbosity of output 0-6')
params = parser.parse_args()
###########################################################################
### CHECK FOR TREE, build if not in place
###########################################################################
if params.tree is None:
from treetime.utils import tree_inference
params.tree = os.path.basename(params.aln) + '.nwk'
print("No tree given: inferring tree")
tmp_dir = 'homoplasy_scanner_tmp_files'
tree_inference(params.aln, params.tree, tmp_dir=tmp_dir)
if os.path.isdir(tmp_dir):
shutil.rmtree(tmp_dir)
###########################################################################
### GTR SET-UP
###########################################################################
model = params.gtr
gtr_params = params.gtr_params
if model == 'infer':
gtr = GTR.standard('jc')
infer_gtr = True
else:
infer_gtr = False
try:
kwargs = {}