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Viewing changes to tests/test_evolve/test_best_likelihood.py

  • Committer: Bazaar Package Importer
  • Author(s): Steffen Moeller
  • Date: 2010-12-04 22:30:35 UTC
  • mfrom: (1.1.1 upstream)
  • Revision ID: james.westby@ubuntu.com-20101204223035-j11kinhcrrdgg2p2
Tags: 1.5-1
* Bumped standard to 3.9.1, no changes required.
* New upstream version.
  - major additions to Cookbook
  - added AlleleFreqs attribute to ensembl Variation objects.
  - added getGeneByStableId method to genome objects.
  - added Introns attribute to Transcript objects and an Intron class.
  - added Mann-Whitney test and a Monte-Carlo version
  - exploratory and confirmatory period estimation techniques (suitable for
    symbolic and continuous data)
  - Information theoretic measures (AIC and BIC) added
  - drawing of trees with collapsed nodes
  - progress display indicator support for terminal and GUI apps
  - added parser for illumina HiSeq2000 and GAiix sequence files as 
    cogent.parse.illumina_sequence.MinimalIlluminaSequenceParser.
  - added parser to FASTQ files, one of the output options for illumina's
    workflow, also added cookbook demo.
  - added functionality for parsing of SFF files without the Roche tools in
    cogent.parse.binary_sff
  - thousand fold performance improvement to nmds
  - >10-fold performance improvements to some Table operations

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tests/test_evolve/test_best_likelihood.py
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__copyright__ = "Copyright 2007-2009, The Cogent Project"
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__credits__ = ["Gavin Huttley", "Helen Lindsay"]
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__license__ = "GPL"
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__version__ = "1.4.1"
 
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__version__ = "1.5.0"
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__maintainer__ = "Helen Lindsay"
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__email__ = "helen.lindsay@anu.edu.au"
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__status__ = "Production"
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                   ['G','T','A'],['G','T','A'],['G','T','A'],
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                   ['T','A','C'],['T','A','C'],['T','A','C'],
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                   ['A','C','G']]
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        assert obs == expect, (obs, expect)
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        obs = aligned_columns_to_rows(self.gapped_aln[:-1], 3)
 
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        self.assertEqual(obs, expect)
 
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        obs = aligned_columns_to_rows(self.gapped_aln[:-1], 3, allowed_chars='ACGT')
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        expect = [['TTT','TAT','TTT']]
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        assert obs == expect, (obs, expect)
 
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        self.assertEqual(obs, expect)
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        obs = aligned_columns_to_rows(self.ambig_aln, 2, IUPAC_DNA_ambiguities)
 
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        obs = aligned_columns_to_rows(self.ambig_aln, 2, exclude_chars=IUPAC_DNA_ambiguities)
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        expect = [['AA','CC','CA'],['CC','CC','CC'],['TT','TT','TG']]
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        assert obs == expect, (obs, expect)
 
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        self.assertEqual(obs, expect)
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    def test_count_column_freqs(self):
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        columns = aligned_columns_to_rows(self.aln, 1)
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        obs = count_column_freqs(columns)
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        expect = {'A C G' : 4, 'C G T' : 3, 'G T A' : 3, 'T A C' : 3}
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        assert obs == expect, (obs, expect)
 
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        self.assertEqual(obs, expect)
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        columns = aligned_columns_to_rows(self.aln[:-1], 2)
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        obs = count_column_freqs(columns)
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        for pattern, lnL, freq in obs:
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            self.assertFloatEqual(lnL, expect[pattern])
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            sum += lnL
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            assert lnL >= 0
 
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            self.assertTrue(lnL >= 0)
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        self.assertFloatEqual(sum, 1)
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    def test_get_G93_lnL_from_array(self):
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        obs = BestLogLikelihood(self.aln, DNA.Alphabet)
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        expect = math.log(math.pow(4/13.0, 4)) + 3*math.log(math.pow(3/13.0, 3))
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        self.assertFloatEqual(obs,expect)
 
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        lnL, l = BestLogLikelihood(self.aln, DNA.Alphabet, return_length=True)
 
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        self.assertEqual(l, len(self.aln))
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if __name__ == '__main__':
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    main()