test_make_bootstrapped_tree.py

#!/usr/bin/env python

__author__ = "Justin Kuczynski"
__copyright__ = "Copyright 2010, The QIIME Project"
__credits__ = ["justin kuczynski"]
__license__ = "GPL"
__version__ = "1.0.0"
__maintainer__ = "Justin Kuczynski"
__email__ = "justinak@gmail.com"
__status__ = "Release"

from qiime.make_bootstrapped_tree import write_pdf_bootstrap_tree
from cogent.util.unit_test import TestCase, main
from cogent.core.tree import PhyloNode
from cogent.parse.tree import DndParser
from cogent.app.util import get_tmp_filename
import os


def remove_files(list_of_filepaths,error_on_missing=True):
    missing = []
    for fp in list_of_filepaths:
        try:
            os.remove(fp)
        except OSError:
            missing.append(fp)

    if error_on_missing and missing:
        raise OSError, "Some filepaths were not accessible: %s"\
            % '\t'.join(missing)

class FunctionTests(TestCase):
    """Tests of top-level functions"""

    def setUp(self):
        self._paths_to_clean_up = []
    def test_write_pdf_bootstrap_tree(self):
        """ write_pdf_bootstrap_tree should throw no errors"""
        
        tree = DndParser(
            "((tax7:0.1,tax3:0.2)node0:.98,tax8:.3, tax4:.3)node1:.4",
            PhyloNode)
        bootstraps = {'node0':.7,'node1':.4}
        f = get_tmp_filename(\
         prefix='make_bootstrapped_tree_test',\
         suffix='.pdf',\
         result_constructor=str)
        self._paths_to_clean_up.append(f)
        write_pdf_bootstrap_tree(tree, f, bootstraps)
        assert(os.path.exists(f))

    def tearDown(self):
        remove_files(self._paths_to_clean_up)
        

#run tests if called from command line
if __name__ == '__main__':
    main()