[Biopython-dev] [Bug 2651] New: Error from test_GAQueens.py

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2651

           Summary: Error from test_GAQueens.py
           Product: Biopython
           Version: 1.49b
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: bsouthey at gmail.com


I got this error with Python2.5 but it is extremely rare. I think that I seen
it before but have never reproduced it. It indicates some bugs are lurking
other than the obvious bug with Seq.py that are being triggered by the test.

======================================================================
ERROR: test_GAQueens                                                  
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Traceback (most recent call last):                                    
  File "run_tests.py", line 125, in runTest                           
    self.runSafeTest()                                                
  File "run_tests.py", line 142, in runSafeTest                       
    cur_test.run_tests([])                                            
  File "test_GAQueens.py", line 42, in run_tests                      
    main(arguments)                                                   
  File "test_GAQueens.py", line 76, in main                           
    evolved_pop = evolver.evolve(queens_solved)                       
  File
"/home/bsouthey/python/biopython-1.49b/build/lib.linux-x86_64-2.5/Bio/GA/Evolver.py",
line 56, in evolve
    self._population = self._selector.select(self._population)                  
  File
"/home/bsouthey/python/biopython-1.49b/build/lib.linux-x86_64-2.5/Bio/GA/Selection/Tournament.py",
line 77, in select
    new_orgs[1])                                                                
  File
"/home/bsouthey/python/biopython-1.49b/build/lib.linux-x86_64-2.5/Bio/GA/Selection/Abstract.py",
line 53, in mutate_and_crossover
    final_org_1 = self._repairer.repair(final_org_1)                            
  File "test_GAQueens.py", line 234, in repair                                  
    duplicated_items = self._get_duplicates(organism.genome)                    
  File "test_GAQueens.py", line 203, in _get_duplicates                         
    if genome.count(item) > 1:                                                  
  File
"/home/bsouthey/python/biopython-1.49b/build/lib.linux-x86_64-2.5/Bio/Seq.py",
line 796, in count                                
    if len(search) == 1 :                                                       
TypeError: object of type 'int' has no len()                                    

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