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example PhylogicNDT/ExampleRuns/PhylogicNDT-Example.ipynb is broken #23

Open judithabk6 opened 4 years ago

judithabk6 commented 4 years ago

command 

!./PhylogicNDT.py Cluster -i Test_Clust -s sample_00:MySimulation_0.txt:None:0.7:0 -s sample_01:MySimulation_1.txt:None:0.7:1 -s sample_02:MySimulation_2.txt:None:0.7:2 -s sample_03:MySimulation_3.txt:None:0.7:3

output

/bioinfo/users/jabecass/dl_tools_centos/PhylogicNDT/phylogicndt.log
Namespace(Delete_Blacklist=False, Pi_k_mu=3, Pi_k_r=3, PoN='false', artifact_blacklist='./data/supplement_data/Blacklist_SNVs.txt', artifact_whitelist='', blacklist_threshold=0.1, buildtree=False, cancer_type='All_cancer', driver_genes_file='./data/supplement_data/Driver_genes_v1.0.txt', func=<function run_tool at 0x7f4dc4c47950>, gistic_fn=None, grid_size=101, html=True, impute_missing=False, indiv_id='Test_Clust', iter=250, maf=False, min_cov=8, n_samples=0, order_by_timepoint=False, sample_data=['sample_00:MySimulation_0.txt:None:0.7:0', 'sample_01:MySimulation_1.txt:None:0.7:1', 'sample_02:MySimulation_2.txt:None:0.7:2', 'sample_03:MySimulation_3.txt:None:0.7:3'], scale=False, seed=None, sif=None, time_points=None, treatment_data=None, tumor_size=None, use_indels=False)
['sample_00:MySimulation_0.txt:None:0.7:0', 'sample_01:MySimulation_1.txt:None:0.7:1', 'sample_02:MySimulation_2.txt:None:0.7:2', 'sample_03:MySimulation_3.txt:None:0.7:3']
Traceback (most recent call last):
  File "./PhylogicNDT.py", line 520, in <module>
    args.func(args)
  File "/bioinfo/users/jabecass/dl_tools_centos/PhylogicNDT/Cluster/Cluster.py", line 75, in run_tool
    purity=purity)
  File "/bioinfo/users/jabecass/dl_tools_centos/PhylogicNDT/data/Patient.py", line 148, in addSample
    purity=purity, timepoint_value=timepoint_value)
  File "/bioinfo/users/jabecass/dl_tools_centos/PhylogicNDT/data/Sample.py", line 91, in __init__
    self.CnProfile = self._resolve_CnEvents(seg_file, input_type=seg_input_type)
  File "/bioinfo/users/jabecass/dl_tools_centos/PhylogicNDT/data/Sample.py", line 507, in _resolve_CnEvents
    raise NotImplementedError('Input file type not supported')
NotImplementedError: Input file type not supported

got it to run with command

!./PhylogicNDT.py Cluster -i Test_Clust -s sample_00:MySimulation_0.txt::0.7:0 -s sample_01:MySimulation_1.txt::0.7:1 -s sample_02:MySimulation_2.txt::0.7:2 -s sample_03:MySimulation_3.txt::0.7:3

as None was casted as a string in variable seg_file, and then if seg_file was used, but returned True, as the string was not empty