work_dir="/path/to/work/dir" ### SET ME input_file="input.bnx" ### SET ME workspace=Workspace(work_dir, input_file) ref_file="reference.cmap" ### SET ME false_positive=0.5 ### SET ME false_negative=0.15 ### SET ME genome_size_mb=900 ### SET ME p_val=1e-05/genome_size_mb min_len=100 ### SET ME min_sites=6 ### SET ME vital_parameters=VitalParameters(false_positive, false_negative, p_val, min_len, min_sites) merge=Merge(workspace, vital_parameters) alignment=ReferenceAlignment(workspace, merge, ref_file) with CD(work_dir): len_file_path=alignment.anchor.getStepDir()+"/"+alignment.output_prefix+".len" with open(len_file_path,'w'): len_file_converter=FileConverter(CmapFile(alignment.anchor.getOutputFile()), LenFile(len_file_path)) len_file_converter.convert() bed_file_path=alignment.getStepDir()+"/"+alignment.output_prefix+".bed" with open(bed_file_path,'w'): pass bed_file_converter=FileConverter(XmapFile(alignment.getOutputFile()), BedFile(bed_file_path)) bed_file_converter.convert()