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Viewing changes to tests/test_core/test_entity.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_core/test_entity.py
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"""
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from copy import deepcopy, copy
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import cPickle
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try:
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    from cogent.util.unit_test import TestCase, main
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    from cogent.core.entity import Atom
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    from cogent.parse.pdb import PDBParser
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except ImportError:
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    from zenpdb.cogent.util.unit_test import TestCase, main
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    from zenpdb.core.entity import Atom
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    from zenpdb.cogent.parse.pdb import PDBParser
 
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from cogent.util.unit_test import TestCase, main
 
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from cogent.core.entity import Atom
 
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from cogent.core.sequence import ProteinSequence
 
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from cogent.parse.pdb import PDBParser
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__author__ = "Marcin Cieslik"
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__copyright__ = "Copyright 2009, The Cogent Project"
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__credits__ = ["Marcin Cieslik"]
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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__ = "Marcin Cieslik"
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__email__ = "mpc4p@virginia.edu"
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__status__ = "Development"
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    def tearDown(self):
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        self.structure = None
 
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    def test_getSeq(self):
 
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        testSeq = self.working_chain.getSeq()
 
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        assert isinstance(testSeq, ProteinSequence)
 
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        assert testSeq == "DKPVAHVVANPQAEGQLQWSNRRANALLANGVELRDNQLVVPIEGL" \
 
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        "FLIYSQVLFKGQGCPSTHVLLTHTISRIAVSYQTKVNLLSAIKSPCQRETPEGAEAKPWYEPI" \
 
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        "YLGGVFQLEKGDRLSAEINRPDYLDFAESGQVYFGIIAL"
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