test_hierarchical_cluster.py

#!/usr/bin/env python

__author__ = "Justin Kuczynski"
__copyright__ = "Copyright 2010, The QIIME Project"
__credits__ = ["justin kuczynski"]
__license__ = "GPL"
__version__ = "0.92"
__maintainer__ = "Justin Kuczynski"
__email__ = "justinak@gmail.com"
__status__ = "Release"

from qiime.hierarchical_cluster import single_file_upgma
from qiime.format import format_distance_matrix
from cogent.util.unit_test import TestCase, main
from cogent.app.util import get_tmp_filename
import os
import numpy

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"""

    def setUp(self):
        self._paths_to_clean_up = []
    def test_single_file_upgma(self):
        """ single_file_upgma should throw no errors"""
        
        titles = ['hi','ho']
        distdata = numpy.array([[0,.5],[.5,0.]])
        fname = get_tmp_filename(prefix='upgma_',suffix='.txt')
        f = open(fname,'w')
        self._paths_to_clean_up.append(fname)
        f.write(format_distance_matrix(titles, distdata))
        f.close()
        
        fname2 = get_tmp_filename(prefix='upgma_',suffix='.txt',
            result_constructor=str)
        self._paths_to_clean_up.append(fname2)
        single_file_upgma(fname,fname2)
        assert(os.path.exists(fname2))

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

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