Python single_file_njの例

コード例 #1

def main():
    option_parser, opts, args = parse_command_line_parameters(**script_info)
    if os.path.isdir(opts.input_path):
        multiple_file_nj(opts.input_path, opts.output_path)
    elif os.path.isfile(opts.input_path):
        single_file_nj(opts.input_path, opts.output_path)
    else:
        print("io error, check input file path")
        exit(1)

コード例 #2

ファイル: neighbor_joining.py プロジェクト: AhmedAbdelfattah/qiime

def main():
    option_parser, opts, args = parse_command_line_parameters(**script_info)
    if os.path.isdir(opts.input_path):
        multiple_file_nj(opts.input_path, opts.output_path)
    elif os.path.isfile(opts.input_path):
        single_file_nj(opts.input_path, opts.output_path)
    else:
        print("io error, check input file path")
        exit(1)

コード例 #3

ファイル: test_hierarchical_cluster.py プロジェクト: qinjunjie/qiime

    def test_single_file_nj(self):
        """ single_file_nj should throw no errors"""

        titles = ["hi", "ho", "yo"]
        distdata = numpy.array([[0, 0.5, 0.3], [0.5, 0.0, 0.9], [0.3, 0.9, 0.0]])
        fname = get_tmp_filename(prefix="nj_", 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="nj_", suffix=".txt", result_constructor=str)
        self._paths_to_clean_up.append(fname2)
        single_file_nj(fname, fname2)
        assert os.path.exists(fname2)

コード例 #4

ファイル: test_hierarchical_cluster.py プロジェクト: Ecogenomics/FrankenQIIME

    def test_single_file_nj(self):
        """ single_file_nj should throw no errors"""

        titles = ['hi','ho','yo']
        distdata = numpy.array([[0,.5,.3],[.5,0.,.9],[.3,.9,0.]])
        fname = get_tmp_filename(prefix='nj_',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='nj_',suffix='.txt',
            result_constructor=str)
        self._paths_to_clean_up.append(fname2)
        single_file_nj(fname,fname2)
        assert(os.path.exists(fname2))

コード例 #5

ファイル: test_hierarchical_cluster.py プロジェクト: rob-knight/qiime

    def test_single_file_nj(self):
        """ single_file_nj should throw no errors"""

        titles = ['hi','ho','yo']
        distdata = numpy.array([[0,.5,.3],[.5,0.,.9],[.3,.9,0.]])
        fname = get_tmp_filename(prefix='nj_',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='nj_',suffix='.txt',
            result_constructor=str)
        self._paths_to_clean_up.append(fname2)
        single_file_nj(fname,fname2)
        assert(os.path.exists(fname2))