Esempio n. 1
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def test_index_missing_application():
    """Test calling index without applying application"""
    from snakemakelib.bio.ngs.db.cloudbiolinux import index

    config = {
        "bio.ngs.settings": {"db": {"build": "hg19", "build_config": None, "ref": "foo.fa"}},
        "bio.ngs.align.bwa": {"index": index},
    }
    bwa_cfg = config["bio.ngs.align.bwa"]
    with pytest.raises(TypeError):
        index(ref=config["bio.ngs.settings"]["db"]["ref"], index=bwa_cfg["index"])
Esempio n. 2
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def test_cloudbiolinux_import():
    """Test that importing cloudbiolinux changes db.index"""
    from snakemakelib.bio.ngs.db import index

    assert "foo.fa" == index("foo.fa", "bar", index="foo.fa")
    import snakemakelib.bio.ngs.db.cloudbiolinux
    from snakemakelib.bio.ngs.db import index

    assert "../bar/foo.fa" == snakemakelib.bio.ngs.db.index("foo.fa", "bar")
    assert "../bar/foo.fa" == index("foo.fa", "bar")
    assert "../bar/foo.fa" == snakemakelib.bio.ngs.db.cloudbiolinux.index("foo.fa", "bar")
Esempio n. 3
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 def test_index(self):
     """Test getting the index for a given application"""
     config = BaseConfig({'bio.ngs.settings' : {'db' : {'build' : 'hg19', 'build_config' : None, 'ref' : self.ref}}, 'bio.ngs.align.bwa': {'index' : ""}})
     cfg = config['bio.ngs.settings']
     bwa_cfg = config['bio.ngs.align.bwa']
     bwa_cfg['index'] =  index(ref= cfg['db']['ref'], index=bwa_cfg['index'], application="bwa")
     self.assertEqual(os.path.normpath(bwa_cfg['index']), os.path.abspath(
         os.path.join(os.curdir, "bwa", "reference")))
Esempio n. 4
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 def test_index_missing_application(self):
     """Test calling index without applying application"""
     config = BaseConfig({'bio.ngs.settings' : {'db' : {'build' : 'hg19', 'build_config' : None, 'ref' : self.ref}}, 'bio.ngs.align.bwa': {'index' : index}})
     bwa_cfg = config['bio.ngs.align.bwa']
     index(ref= config['bio.ngs.settings']['db']['ref'], index=bwa_cfg['index'])
Esempio n. 5
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def test_index():
    assert "foo.fa" == index("foo.fa", "bar")