コード例 #1
0
ファイル: wrappers.py プロジェクト: junhuili/treetime
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
コード例 #2
0
ファイル: wrappers.py プロジェクト: neherlab/treetime
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
コード例 #3
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 = {}