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brettc / partitionfinder

PartitionFinder discovers optimal partitioning schemes for DNA sequences.
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bug in rcluster #62

Closed roblanf closed 8 years ago

roblanf commented 9 years ago

Karen et al have a case where rcluster does something I don't understand. The error is in neighbour.py reset_subsets():

DEBUG    | 2015-08-16 01:41:34,224 | scheme     | Grand total parameters: 1180
DEBUG    | 2015-08-16 01:41:34,224 | scheme     | n: 6752 K: 1180 lnL: -236797
INFO     | 2015-08-16 01:41:34,224 | analysis_m | The best scheme improves the aicc score by 897.83 to 475556.6
DEBUG    | 2015-08-16 01:41:34,231 | config     | Returning to original path: /home/meu00c/CSIRO/1KITE_analyses_Neuropterida_2015/PF
DEBUG    | 2015-08-16 01:41:34,231 | config     | Cleaning out all subsets (There are 422)...
Traceback (most recent call last):
  File "/home/meu00c/CSIRO/Programs/PF/partitionfinder-2.0-pre1/PartitionFinderProtein.py", line 23, in <module>
    sys.exit(main.main("PartitionFinderProtein", "protein"))
  File "/home/meu00c/CSIRO/Programs/PF/partitionfinder-2.0-pre1/partfinder/main.py", line 370, in main
    run_analysis(cfg, options)
  File "/home/meu00c/CSIRO/Programs/PF/partitionfinder-2.0-pre1/partfinder/main.py", line 306, in run_analysis
    results = anal.analyse()
  File "/home/meu00c/CSIRO/Programs/PF/partitionfinder-2.0-pre1/partfinder/analysis.py", line 91, in analyse
    self.do_analysis()
  File "/home/meu00c/CSIRO/Programs/PF/partitionfinder-2.0-pre1/partfinder/analysis_method.py", line 367, in do_analysis
    subsets = neighbour.reset_subsets(subsets, list(best_pair), [best_merged])
  File "/home/meu00c/CSIRO/Programs/PF/partitionfinder-2.0-pre1/partfinder/neighbour.py", line 244, in reset_subsets
    subsets.pop(subsets.index(r))
ValueError: Subset(EOG73..) is not in list
roblanf commented 8 years ago

fixed