def setUp(self):
self.workspace=Workspace(self.saved_path + "/test_work_dir", "input.bnx")
os.mkdir(self.workspace.work_dir)
os.chdir(self.workspace.work_dir)
with open(self.workspace.input_file, "w") as bnx_file:
bnx_file.write("\n".join([
"# BNX File Version: 1.2",
"#0h LabelChannel MoleculeId Length AvgIntensity SNR NumberofLabels OriginalMoleculeId ScanNumber ScanDirection ChipId Flowcell RunId GlobalScanNumber",
"#0f int int float float float int int int int string int int int",
"#1h LabelChannel LabelPositions[N]",
"#1f int float",
"#2h LabelChannel LabelPositions[N]",
"#2h int float",
"#Qh QualityScoreID QualityScores[N]",
"#Qf str float",
"0 1 11915.3 0.064331 39.060 7 1 1 -1 20249,11731,11/25/2013,840012494 1 1 1",
"1 0.0 3785.6 5068.4 7060.8 7968.7 7987.8 11267.0 11915.3",
"QX11 0.6905 0.8113 0.5751 1.4108 2.2148 1.1966 0.8701",
"QX12 0.0327 0.0330 0.0328 0.0342 0.0349 0.0341 0.0334"
]))
self.workspace.addBinary("bng_assembler", "path/to/Assembler")
self.workspace.addBinary("bng_ref_aligner", "path/to/RefAligner")
self.buffer_stdout=StringIO.StringIO()
sys.stdout=self.buffer_stdout
from Operations.BioNano.Assemble.RefineB0 import RefineB0
from Operations.BioNano.Assemble.Assembly import RefineA
from Operations.BioNano.Assemble.Merge import Merge
from Operations.BioNano.Assemble.Assembly import Assembly
from Operations.BioNano.Assemble.PairwiseAlignment import PairwiseAlignment
from Operations.BioNano.Assemble.Split import Split
from Operations.BioNano.Assemble.Sort import Sort
from Operations.BioNano.Assemble.VitalParameters import VitalParameters
from Utils.Workspace import Workspace
from Utils.CD import CD
from Operations.SBATCHCodeFormatter import CodeFormatter
work_dir="/path/to/work/dir/" ### SET ME
input_file="input_file.bnx" ### SET ME
workspace=Workspace(work_dir, input_file)
workspace.errorNotificationEmail='*****@*****.**' ### SET ME
workspace.addBinary("bng_assembler", "/path/to/Assembler") ### SET ME
workspace.addBinary("bng_ref_aligner", "/path/to/RefAligner") ### SET ME
false_positives=1.5 ### SET ME
false_negatives=.386 ### SET ME
p_val_cutoff=1.11e-6 ### SET ME
min_molecule_len=100 ### SET ME
min_molecule_sites=10 ### SET ME
vital_parameters=VitalParameters(false_positives, false_negatives, p_val_cutoff, min_molecule_len, min_molecule_sites)
step=Assembly(workspace, vital_parameters) ### SET ME: see options below
### RefineB0, RefineA, Merge, Assembly, PairwiseAlignment, Split, or Sort
class SmokeTest(unittest.TestCase):
vital_parameters=VitalParameters(1.5, .150, 1e-5, 100, 6)
formatter=CodeFormatter()
native_stdout=sys.stdout
saved_path=os.getcwd()
def setUp(self):
self.workspace=Workspace(self.saved_path + "/test_work_dir", "input.bnx")
os.mkdir(self.workspace.work_dir)
os.chdir(self.workspace.work_dir)
with open(self.workspace.input_file, "w") as bnx_file:
bnx_file.write("\n".join([
"# BNX File Version: 1.2",
"#0h LabelChannel MoleculeId Length AvgIntensity SNR NumberofLabels OriginalMoleculeId ScanNumber ScanDirection ChipId Flowcell RunId GlobalScanNumber",
"#0f int int float float float int int int int string int int int",
"#1h LabelChannel LabelPositions[N]",
"#1f int float",
"#2h LabelChannel LabelPositions[N]",
"#2h int float",
"#Qh QualityScoreID QualityScores[N]",
"#Qf str float",
"0 1 11915.3 0.064331 39.060 7 1 1 -1 20249,11731,11/25/2013,840012494 1 1 1",
"1 0.0 3785.6 5068.4 7060.8 7968.7 7987.8 11267.0 11915.3",
"QX11 0.6905 0.8113 0.5751 1.4108 2.2148 1.1966 0.8701",
"QX12 0.0327 0.0330 0.0328 0.0342 0.0349 0.0341 0.0334"
]))
self.workspace.addBinary("bng_assembler", "path/to/Assembler")
self.workspace.addBinary("bng_ref_aligner", "path/to/RefAligner")
self.buffer_stdout=StringIO.StringIO()
sys.stdout=self.buffer_stdout
def tearDown(self):
self.buffer_stdout.close()
sys.stdout=self.native_stdout
os.chdir(self.saved_path)
shutil.rmtree(self.workspace.work_dir)
def dummy_returnTrue(self):
return True
def dummy_returnFalse(self):
return False
def test_writeCode_sort(self):
step=Sort(self.workspace, copy(self.vital_parameters))
expected="\n".join(["#!/bin/bash",
"",
"",
"step1=\"-d afterok\"",
"sresult=`sbatch step1_part1.sh`",
"echo $sresult",
"sid=`echo $sresult | awk '{print $NF}'`",
"step1=$step1:$sid",
""
])
self.formatter.runOneStep(step)
self.assertEqual(expected, self.buffer_stdout.getvalue())
def test_writeCode_sort_isComplete(self):
native_isComplete=Sort.isComplete
Sort.isComplete=self.dummy_returnTrue.im_func
step=Sort(self.workspace, copy(self.vital_parameters))
expected="\n".join(["#!/bin/bash",
"",
""
])
self.formatter.runOneStep(step)
Sort.isComplete=native_isComplete
self.assertEqual(expected, self.buffer_stdout.getvalue())
def test_writeCode_assembly(self):
step=Assembly(self.workspace, copy(self.vital_parameters))
expected="\n".join(["#!/bin/bash",
"",
"",
"step1=\"-d afterok\"",
"sresult=`sbatch step1_part1.sh`",
"echo $sresult",
"sid=`echo $sresult | awk '{print $NF}'`",
"step1=$step1:$sid",
"",
"step2=\"-d afterok\"",
"sresult=`sbatch $step1 step2_part1.sh`",
"echo $sresult",
"sid=`echo $sresult | awk '{print $NF}'`",
"step2=$step2:$sid",
"",
"step3=\"-d afterok\"",
"sresult=`sbatch $step2 step3_part1.sh`",
"echo $sresult",
"sid=`echo $sresult | awk '{print $NF}'`",
"step3=$step3:$sid",
"",
"step4=\"-d afterok\"",
"sresult=`sbatch $step3 step4_part1.sh`",
"echo $sresult",
"sid=`echo $sresult | awk '{print $NF}'`",
"step4=$step4:$sid",
"",
"step5=\"-d afterok\"",
"sresult=`sbatch $step4 step5_part1.sh`",
"echo $sresult",
"sid=`echo $sresult | awk '{print $NF}'`",
"step5=$step5:$sid",
"",
"step6=\"-d afterok\"",
"sresult=`sbatch $step5 step6_part1.sh`",
"echo $sresult",
"sid=`echo $sresult | awk '{print $NF}'`",
"step6=$step6:$sid",
""
])
self.formatter.runOneStep(step)
self.assertEqual(expected, self.buffer_stdout.getvalue())
def test_parameterSearch(self):
search=ParameterSearch(self.workspace, 900)
expected_lines={
"total": 2559,
"blank": 428,
"level6": 405,
"sbatch_$level5": 405,
"level5": 9,
"sbatch_$level4": 9,
"level4": 9,
"sbatch_$level3": 9,
"level3": 1,
"sbatch_$level2": 1,
"level2": 1,
"sbatch_$level1": 1,
"level1": 1,
"sbatch__level1": 1
}
BLANK=re.compile("^$")
LEVEL6=re.compile("level6_.*=\"-d afterok\"")
LEVEL5=re.compile("level5_.*=\"-d afterok\"")
LEVEL4=re.compile("level4_.*=\"-d afterok\"")
LEVEL3=re.compile("level3_.*=\"-d afterok\"")
LEVEL2=re.compile("level2_.*=\"-d afterok\"")
LEVEL1=re.compile("level1_.*=\"-d afterok\"")
SBATCH_LEVEL5=re.compile("sbatch \$level5")
SBATCH_LEVEL4=re.compile("sbatch \$level4")
SBATCH_LEVEL3=re.compile("sbatch \$level3")
SBATCH_LEVEL2=re.compile("sbatch \$level2")
SBATCH_LEVEL1=re.compile("sbatch \$level1")
SBATCH_NADA=re.compile("sbatch level1_")
self.formatter.runSeveralSteps(search.writeCode())
actual_lines={
"total": 0,
"blank": 0,
"level6": 0,
"sbatch_$level5": 0,
"level5": 0,
"sbatch_$level4": 0,
"level4": 0,
"sbatch_$level3": 0,
"level3": 0,
"sbatch_$level2": 0,
"level2": 0,
"sbatch_$level1": 0,
"level1": 0,
"sbatch__level1": 0
}
output=self.buffer_stdout.getvalue()
for line in output.split("\n"):
actual_lines["total"]+=1
if BLANK.search(line) is not None:
actual_lines["blank"]+=1
if LEVEL6.search(line) is not None:
actual_lines["level6"]+=1
if LEVEL5.search(line) is not None:
actual_lines["level5"]+=1
if LEVEL4.search(line) is not None:
actual_lines["level4"]+=1
if LEVEL3.search(line) is not None:
actual_lines["level3"]+=1
if LEVEL2.search(line) is not None:
actual_lines["level2"]+=1
if LEVEL1.search(line) is not None:
actual_lines["level1"]+=1
if SBATCH_LEVEL5.search(line) is not None:
actual_lines["sbatch_$level5"]+=1
if SBATCH_LEVEL4.search(line) is not None:
actual_lines["sbatch_$level4"]+=1
if SBATCH_LEVEL3.search(line) is not None:
actual_lines["sbatch_$level3"]+=1
if SBATCH_LEVEL2.search(line) is not None:
actual_lines["sbatch_$level2"]+=1
if SBATCH_LEVEL1.search(line) is not None:
actual_lines["sbatch_$level1"]+=1
if SBATCH_NADA.search(line) is not None:
actual_lines["sbatch__level1"]+=1
self.maxDiff=None
self.assertEqual(expected_lines, actual_lines)
