#!/usr/bin/python
# The purpose of this script is to run an automated param search
from Operations.BioNano.Parameterize.ParameterSearch import ParameterSearch
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
genome_size_mb=900 ### SET ME
parameter_search=ParameterSearch(workspace, genome_size_mb)
#average_label_density=7.0 ### SET ME MAYBE
#expected_label_density=13.5 ### SET ME MAYBE
#parameter_search.optimizeFalsehoods(average_label_density, expected_label_density) ### UNCOMMENT ME MAYBE
#parameter_search.autoGeneratePrereqs() ### UNCOMMENT ME MAYBE
with CD(work_dir):
formatter=CodeFormatter()
formatter.runSeveralSteps(parameter_search.writeCode())
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)