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())