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Viewing changes to tests/test_db/test_ensembl/test_database.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_db/test_ensembl/test_database.py
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__copyright__ = "Copyright 2007-2009, The Cogent Project"
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__credits__ = ["Gavin Huttley", "hua Ying"]
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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__ = "Gavin Huttley"
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__email__ = "Gavin.Huttley@anu.edu.au"
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__status__ = "alpha"
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Release = 56
 
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Release = 58
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if 'ENSEMBL_ACCOUNT' in os.environ:
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    username, password = os.environ['ENSEMBL_ACCOUNT'].split()
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        db = Database(account=account, release=Release, db_type='compara')
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        got = set(db.getDistinct('homology', 'description'))
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        expected = set(['apparent_ortholog_one2one', 'between_species_paralog',
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        'ortholog_many2many', 'ortholog_one2many', 'ortholog_one2one',
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        'within_species_paralog'])
 
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        expected = set(['apparent_ortholog_one2one', 'ortholog_many2many',
 
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          'ortholog_one2many', 'ortholog_one2one', 'within_species_paralog'])
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        self.assertEquals(len(got&expected), len(expected))
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    def test_get_table_row_counts(self):
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        """should return correct row counts for some tables"""
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        expect = {'homo_sapiens_core_56_37a.analysis': 57L,
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                  'homo_sapiens_core_56_37a.seq_region': 55604L,
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                  'homo_sapiens_core_56_37a.assembly': 102068L,
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                  'homo_sapiens_core_56_37a.qtl': 0L}
 
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        expect = {'homo_sapiens_core_58_37c.analysis': 61L,
 
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                  'homo_sapiens_core_58_37c.seq_region': 55616L,
 
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                  'homo_sapiens_core_58_37c.assembly': 102090L,
 
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                  'homo_sapiens_core_58_37c.qtl': 0L}
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        human = Database(account=account, release=Release,
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                    species='human', db_type='core')
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        table_names = [n.split('.')[1] for n in expect]