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Viewing changes to tests/test_parse/test_structure.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_parse/test_structure.py
 
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#!/usr/bin/env python
 
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"""Unit tests for the pdb parser.
 
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"""
 
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from cogent.util.unit_test import TestCase, main
 
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from cogent.core.entity import Structure
 
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from cogent.parse.structure import FromFilenameStructureParser, FromFileStructureParser
 
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__author__ = "Marcin Knight"
 
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__copyright__ = "Copyright 2007-2009, The Cogent Project"
 
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__credits__ = ["Marcin Cieslik"]
 
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__license__ = "GPL"
 
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__version__ = "1.5.0"
 
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__maintainer__ = "Marcin Cieslik"
 
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__email__ = "mpc4p@virginia.edu"
 
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__status__ = "Production"
 
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class structuresTests(TestCase):
 
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    """Tests of cogent.parse.structure UI functions."""
 
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    def test_FromFilenameStructureParser(self):
 
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        structure = FromFilenameStructureParser('data/1LJO.pdb', 'pdb')
 
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        self.assertRaises(TypeError, FromFilenameStructureParser, open('data/1LJO.pdb'), 'pdb')
 
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        assert isinstance(structure, Structure)
 
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    def test_FromFileStructureParser(self):
 
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        structure = FromFileStructureParser(open('data/1LJO.pdb'), 'pdb')
 
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        assert isinstance(structure, Structure)
 
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        self.assertRaises(TypeError, FromFileStructureParser, 'data/1LJO.pdb', 'pdb')
 
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        assert isinstance(structure, Structure)         
 
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if __name__ == '__main__':
 
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    main()