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
with CD(work_dir):
formatter=CodeFormatter()
formatter.runOneStep(step)
#!/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())
