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"])
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")
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")))
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'])
def test_index():
assert "foo.fa" == index("foo.fa", "bar")