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  • 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_maths/test_stats/test_alpha_diversity.py
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#!/usr/bin/env python
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#file test_alpha_diversity.py
 
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from __future__ import division
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from numpy import array, log, sqrt, exp
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from math import e
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from cogent.util.unit_test import TestCase, main
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    strong, kempton_taylor_q, fisher_alpha, \
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    mcintosh_e, heip_e, simpson_e, robbins, robbins_confidence, \
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    chao1_uncorrected, chao1_bias_corrected, chao1, chao1_var, \
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    chao1_confidence, ACE
 
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    chao1_confidence, ACE, michaelis_menten_fit
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__author__ = "Rob Knight"
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__copyright__ = "Copyright 2007-2009, The Cogent Project"
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__credits__ = ["Rob Knight"]
 
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__credits__ = ["Rob Knight","Justin Kuczynski"]
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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__ = "Rob Knight"
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__email__ = "rob@spot.colorado.edu"
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__status__ = "Production"
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        self.assertFloatEqual(ACE(array([12,3,2,1])), 4.6, eps=0.001)
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        self.assertFloatEqual(ACE(array([12,3,6,1,10])), 5.62749672, eps=0.001)
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    def test_michaelis_menten_fit(self):
 
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        """ michaelis_menten_fit should match hand values in limiting cases"""
 
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        res = michaelis_menten_fit([22])
 
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        self.assertFloatEqual(res,1.0,eps=.01)
 
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        res =  michaelis_menten_fit([42])
 
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        self.assertFloatEqual(res,1.0,eps=.01)
 
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        res =  michaelis_menten_fit([34],num_repeats=3,params_guess=[13,13])
 
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        self.assertFloatEqual(res,1.0,eps=.01)
 
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        res =  michaelis_menten_fit([70,70],num_repeats=5)
 
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        self.assertFloatEqual(res,2.0,eps=.01)
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if __name__ == '__main__':