def test_init_with_algorithmOptions(self):
"""Test PBAlign.__init__() with --algorithmOptions."""
argumentList = [
"--algorithmOptions",
"-minMatch 10 -useccsall",
self.queryFile,
self.referenceFile,
self.cmph5Out,
]
pbobj = PBAlign(argumentList=argumentList)
self.assertEqual(pbobj.start(), 0)
def test_init_with_config_algorithmOptions(self):
"""Test PBAlign.__init__() with a config file and --algorithmOptions."""
argumentList = [
"--algorithmOptions",
"-maxMatch 20 -nCandidates 30",
"--configFile",
self.configFile,
self.queryFile,
self.referenceFile,
self.cmph5Out,
]
pbobj = PBAlign(argumentList=argumentList)
self.assertEqual(pbobj.start(), 0)
def test_init_expect_conflicting_options(self):
"""Test PBAlign.__init__() with a config file and --algorithmOptions
and expect a ValueError for conflicting options."""
argumentList = [
"--algorithmOptions",
"-minMatch 10 -useccsall",
"--configFile",
self.configFile,
self.queryFile,
self.referenceFile,
self.cmph5Out,
]
pbobj = PBAlign(argumentList=argumentList)
with self.assertRaises(ValueError) as cm:
# Expect a ValueError since -minMatch and --minAnchorSize conflicts.
pbobj.start()
# * Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and/or other materials provided with the distribution.
# * Neither the name of Pacific Biosciences nor the names of its
# contributors may be used to endorse or promote products derived from
# this software without specific prior written permission.
#
# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
# THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS
# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT
# NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR
# ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
###############################################################################
# Author: Yuan Li
"""This script creates a PBAlign object and start to align reads."""
import sys
from pbtools.pbalign.pbalign import PBAlign
if __name__ == "__main__":
ALIGNER = PBAlign(sys.argv[1:])
sys.exit(ALIGNER.start())
def test_init(self):
"""Test PBAlign.__init__()."""
argumentList = ["--minAccuracy", "70", "--maxDivergence", "30", self.queryFile, self.referenceFile, self.samOut]
pbobj = PBAlign(argumentList=argumentList)
self.assertEqual(pbobj.start(), 0)