def writeCode(self):
run_assemblies=set()
assembly_summaries=set()
run_merges=set()
run_ref_alignment_inputs=set()
run_ref_alignments=set()
run_ref=None
for assembly in self.assemblies:
if not assembly.isComplete():
run_assemblies.add(assembly)
assembly_summaries.add(Summarize(self.workspace, assembly))
merge=Merge(self.workspace, assembly)
if not merge.isComplete():
run_merges.add(merge)
if hasattr(self, "ref_file_name"):
ref_alignment=ReferenceAlignment(self.workspace, merge, self.ref_file_name)
if not ref_alignment.isComplete():
run_ref_alignments.add(ref_alignment)
ref_alignment_input=ref_alignment.query
if not ref_alignment_input.isComplete():
run_ref_alignment_inputs.add(ref_alignment_input)
run_ref=ref_alignment.anchor
necessary_sorts=set()
necessary_splits=set()
necessary_pas=set()
for assembly in run_assemblies:
self.educateAssembly(assembly)
necessary_sorts.add(assembly.sort)
necessary_splits.add(assembly.split)
necessary_pas.add(assembly.pairwise_alignment)
run_sorts=set()
for sort in necessary_sorts:
if not sort.isComplete():
run_sorts.add(sort)
run_splits=set()
split_summaries=set()
for split in necessary_splits:
if not split.isComplete():
run_splits.add(split)
split_summaries.add(Summarize(self.workspace, split))
run_pas=set()
pairwise_summaries=set()
for pairwise in necessary_pas:
if not pairwise.isComplete():
run_pas.add(pairwise)
pairwise_summaries.add(Summarize(self.workspace, pairwise))
return [run_sorts,run_splits,split_summaries,run_pas,pairwise_summaries,run_assemblies,assembly_summaries,run_merges,[run_ref],run_ref_alignment_inputs,run_ref_alignments]
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()
