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Viewing changes to tests/test_cluster/test_metric_scaling.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_cluster/test_metric_scaling.py
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__author__ = "Catherine Lozupone"
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__copyright__ = "Copyright 2007-2009, The Cogent Project"
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__credits__ = ["Catherine Lozupone", "Peter Maxwell", "Rob Knight",
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                "Justin Kuczynski"]
 
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                "Justin Kuczynski", "Daniel McDonald"]
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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__ = "Catherine Lozupone"
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__email__ = "lozupone@colorado.edu"
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__status__ = "Production"
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    def test_make_F_matrix(self):
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        """make_F_matrix converts an E_matrix to an F_matrix"""
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        matrix = self.matrix
 
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        #matrix = self.matrix
 
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        matrix = array([[1,2,3],[4,5,6],[7,8,9]])
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        F_matrix = make_F_matrix(matrix)
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        self.assertEqual(F_matrix, array([[0.0, 0.0, 0.0], [0.0, 0.0, 0.0]]))
 
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        self.assertEqual(F_matrix, array([[0.0, -2.0, -4.0], 
 
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                                          [2.0, 0.0, -2.0],
 
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                                          [4.0, 2.0, 0.0]]))
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    def test_run_eig(self):
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        """run_eig returns eigenvectors and values"""