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broadinstitute / PhylogicNDT

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About SinglePatientTiming demo #67

Open RetGiraffe11235 opened 11 months ago

RetGiraffe11235 commented 11 months ago

Hi Developer,

Thank you for developing such a valuable tool. I apologize for my limited understanding, but could you guide me on how to run SinglePatientTiming using the example data? I tried to execute it using the SegFile in ExampleData, but it wasn't successful. It would be greatly appreciated if you could provide sample data specifically for SinglePatientTiming. Thank you for your great effort in maintaining this tool.

Best, Tomoki

iglc commented 10 months ago

Please first run the Clustering and Build tree tools.

TomokiMotegi commented 8 months ago

Hi iglc, Thank you for your reply. I have completed the clustering and constructed the tree via singularity using original samples. Then, I made seg files from get_CN_Absolute.Phylogic_SinglePatientTiming.R and I tried to run Timing but encountered an issue. The error message is below. "Traceback (most recent call last): File "/phylogicndt/PhylogicNDT.py", line 515, in args.func(args) File "/phylogicndt/SinglePatientTiming/SinglePatientTiming.py", line 28, in run_tool purity=purity) File "/phylogicndt/data/Patient.py", line 148, in addSample purity=purity, timepoint_value=timepoint_value) File "/phylogicndt/data/Sample.py", line 92, in init _additional_muts=_additional_muts) # a list of SomMutation objects File "/phylogicndt/data/Sample.py", line 139, in _load_sample_ccf mut_with_ccf_dat = self._read_post_clustering_results(filen) File "/phylogicndt/data/Sample.py", line 219, in _read_post_clustering_results sample_id = values[header['Sample_ID']] UnboundLocalError: local variable 'header' referenced before assignment"

Could you please provide guidance on resolving this error?