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Viewing changes to tests/test_beta_metrics.py

  • Committer: Package Import Robot
  • Author(s): Andreas Tille
  • Date: 2013-06-17 18:28:26 UTC
  • mfrom: (9.1.2 sid)
  • Revision ID: package-import@ubuntu.com-20130617182826-376az5ad080a0sfe
Tags: 1.7.0+dfsg-1
Upload preparations done for BioLinux to Debian

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tests/test_beta_metrics.py
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__copyright__ = "Copyright 2011, The QIIME Project"
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__credits__ = ["Rob Knight", "Justin Kuczynski"]
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__license__ = "GPL"
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__version__ = "1.5.0"
 
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__version__ = "1.7.0"
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__maintainer__ = "justin kuczynski"
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__email__ = "justinak@gmail.com"
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__status__ = "Release"
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from cogent.util.unit_test import TestCase, main
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from cogent.maths.unifrac.fast_unifrac import fast_unifrac
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from qiime.parse import make_envs_dict
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from qiime.beta_metrics import (_reorder_unifrac_res, make_unifrac_metric)
 
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from qiime.beta_metrics import (_reorder_unifrac_res, make_unifrac_metric, make_unifrac_row_metric)
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from qiime.parse import parse_newick
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from cogent.core.tree import PhyloNode
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from cogent.maths.unifrac.fast_tree import (unifrac)
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        self.assertEqual(res[0,0], 0)
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        self.assertEqual(res[0,3], 0.0)
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        self.assertEqual(res[0,1], 1.0)
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    def test_make_unifrac_row_metric3(self):
 
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        treestr = '((((tax7:0.1):.98,tax8:.3, tax4:.3):.4, '+\
 
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            '((tax6:.09):0.43):0.5):.2,'+\
 
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            '(tax9:0.3, endbigtaxon:.08));' # taxa 1,2,3 removed
 
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        tree = parse_newick(treestr, PhyloNode)
 
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        otu_data = numpy.array([
 
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            [7,1,0,0,0,0,0,0,0], # 1 now zeros
 
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            [4,2,0,0,0,1,0,0,0], 
 
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            [2,4,0,0,0,1,0,0,0],
 
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            [1,7,0,0,0,0,0,0,0], # 4 now zeros
 
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            [0,8,0,0,0,0,0,0,0],
 
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            [0,7,1,0,0,0,0,0,0],
 
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            [0,4,2,0,0,0,2,0,0],
 
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            [0,2,4,0,0,0,1,0,0],
 
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            [0,1,7,0,0,0,0,0,0],
 
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            [0,0,8,0,0,0,0,0,0],
 
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            [0,0,7,1,0,0,0,0,0],
 
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            [0,0,4,2,0,0,0,3,0],
 
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            [0,0,2,4,0,0,0,1,0],
 
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            [0,0,1,7,0,0,0,0,0],
 
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            [0,0,0,8,0,0,0,0,0],
 
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            [0,0,0,7,1,0,0,0,0],
 
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            [0,0,0,4,2,0,0,0,4],
 
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            [0,0,0,2,4,0,0,0,1],
 
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            [0,0,0,1,7,0,0,0,0]
 
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            ])
 
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        unif = make_unifrac_metric(False, unifrac, True)
 
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        warnings.filterwarnings('ignore')
 
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        res = unif(otu_data, self.l19_taxon_names, tree,
 
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            self.l19_sample_names)
 
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        warnings.resetwarnings()
 
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        envs = make_envs_dict(self.l19_data, self.l19_sample_names,
 
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            self.l19_taxon_names)
 
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        self.assertEqual(res[0,0], 0)
 
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        self.assertEqual(res[0,3], 0.0)
 
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        self.assertEqual(res[0,1], 1.0)
 
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        warnings.filterwarnings('ignore')
 
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        unif_row = make_unifrac_row_metric(False, unifrac, True)
 
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        for i, sam_name in enumerate(self.l19_sample_names):
 
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            if i in [0,3,4,5,8,9]: continue 
 
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            # these have no data and are warned "meaningless".
 
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            # I Would prefer if they matched res anyway though
 
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            res_row = unif_row(otu_data, self.l19_taxon_names, tree,
 
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            self.l19_sample_names, sam_name)
 
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            for j in range(len(self.l19_sample_names)):
 
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                if j in [0,3,4,5,8,9]: continue # ok if meaningless number in zero sample
 
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                self.assertEqual(res_row[j], res[i,j])
 
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        warnings.resetwarnings()
 
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    def test_make_unifrac_row_metric2(self):
 
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        """ samples with no seqs, and identical samples, should behave correctly
 
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        """
 
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        tree = parse_newick(self.l19_treestr, PhyloNode)
 
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        unif = make_unifrac_metric(False, unifrac, True)
 
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        otu_data = numpy.array([
 
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            [0,0,0,0,0,0,0,0,0],#sam1 zeros
 
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            [4,2,0,0,0,1,0,0,0],
 
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            [2,4,0,0,0,1,0,0,0],
 
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            [1,7,0,0,0,0,0,0,0],
 
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            [0,8,0,0,0,0,0,0,0],
 
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            [0,7,1,0,0,0,0,0,0],
 
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            [0,4,2,0,0,0,2,0,0],
 
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            [0,2,4,0,0,0,1,0,0],
 
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            [0,1,7,0,0,0,0,0,0],
 
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            [0,0,8,0,0,0,0,0,0],
 
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            [0,0,7,1,0,0,0,0,0],
 
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            [0,0,4,2,0,0,0,3,0],
 
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            [0,0,2,4,0,0,0,1,0],
 
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            [0,0,0,0,0,0,0,0,0],#sam14 zeros
 
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            [0,0,0,8,0,0,0,0,0],
 
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            [0,0,2,4,0,0,0,1,0], #sam 16 now like sam 13
 
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            [0,0,0,4,2,0,0,0,4],
 
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            [0,0,0,2,4,0,0,0,1],
 
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            [0,0,0,1,7,0,0,0,0]
 
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            ])
 
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        warnings.filterwarnings('ignore')
 
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        res = unif(otu_data, self.l19_taxon_names, tree,
 
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            self.l19_sample_names)
 
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        envs = make_envs_dict(self.l19_data, self.l19_sample_names,
 
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            self.l19_taxon_names)
 
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        self.assertEqual(res[0,0], 0)
 
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        self.assertEqual(res[0,13], 0.0)
 
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        self.assertEqual(res[12,15], 0.0)
 
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        self.assertEqual(res[0,1], 1.0)
 
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        warnings.resetwarnings()
 
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        warnings.filterwarnings('ignore')
 
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        unif_row = make_unifrac_row_metric(False, unifrac, True)
 
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        for i, sam_name in enumerate(self.l19_sample_names):
 
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            if i in [0]: continue 
 
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            # these have no data and are warned "meaningless".
 
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            # I Would prefer if they matched res anyway though
 
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            res_row = unif_row(otu_data, self.l19_taxon_names, tree,
 
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            self.l19_sample_names, sam_name)
 
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            for j in range(len((self.l19_sample_names))):
 
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                if j in [0]: continue # ok if meaningless number in zero sample
 
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                self.assertEqual(res_row[j], res[i,j])
 
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        warnings.resetwarnings()
 
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#run tests if called from command line
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if __name__ == '__main__':
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    main()