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()
