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src/q/i/qiime-1.8.0/scripts/beta_significance.py   qiime(Download)
import warnings
warnings.filterwarnings('ignore', 'Not using MPI as mpi4py not found')
from cogent.maths.unifrac.fast_unifrac import fast_unifrac_permutations_file, TEST_ON_PAIRWISE, TEST_ON_TREE, TEST_ON_ENVS
from cogent.maths.unifrac.fast_unifrac import fast_p_test_file
from qiime.util import parse_command_line_parameters
        envs_in = open(output_fp,'U')
 
        result = fast_unifrac_permutations_file(tree_in, envs_in,
            weighted=False, num_iters=opts.num_iters, verbose=opts.verbose, test_on=type_of_test)
        envs_in.close()
        envs_in = open(output_fp,'U')
 
        result = fast_unifrac_permutations_file(tree_in, envs_in,
            weighted=True, num_iters=opts.num_iters, verbose=opts.verbose, test_on=type_of_test)
        envs_in.close()
		envs_in = open(output_fp, 'U')
 
		result = fast_unifrac_permutations_file(tree_in, envs_in,
			weighted='correct', num_iters = opts.num_iters, verbose=opts.verbose, test_on=type_of_test)
		envs_in.close()

src/q/i/qiime-HEAD/scripts/beta_significance.py   qiime(Download)
import warnings
warnings.filterwarnings('ignore', 'Not using MPI as mpi4py not found')
from cogent.maths.unifrac.fast_unifrac import fast_unifrac_permutations_file, TEST_ON_PAIRWISE, TEST_ON_TREE, TEST_ON_ENVS
from cogent.maths.unifrac.fast_unifrac import fast_p_test_file
from qiime.util import parse_command_line_parameters
        envs_in = open(output_fp, 'U')
 
        result = fast_unifrac_permutations_file(tree_in, envs_in,
                                                weighted=False, num_iters=opts.num_iters, verbose=opts.verbose, test_on=type_of_test)
        envs_in.close()
        envs_in = open(output_fp, 'U')
 
        result = fast_unifrac_permutations_file(tree_in, envs_in,
                                                weighted=True, num_iters=opts.num_iters, verbose=opts.verbose, test_on=type_of_test)
        envs_in.close()
        envs_in = open(output_fp, 'U')
 
        result = fast_unifrac_permutations_file(tree_in, envs_in,
                                                weighted='correct', num_iters=opts.num_iters, verbose=opts.verbose, test_on=type_of_test)
        envs_in.close()