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tests.print_paths()   A

↳ Parent: Project

Complexity

Conditions 3

Size

Total Lines 5

Duplication

Lines 0
Ratio 0 %
Metric Value
cc 3
dl 0
loc 5
rs 9.4285
1 
import sys
2 
import os
3 
from goatools.obo_parser import GODag
4 

            


            
                                                                                                            
                            
            
                                    
            
            

                
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ROOT = os.path.dirname(os.path.abspath(__file__)) + "/data/"

            


            
                                                                                                            
                            
            
                                    
            
            

                
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def print_paths(paths, PRT=sys.stdout):

            


            
                                                                        
                            
            
                                    
            
            

                
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    for path in paths:

            


            
                                                                        
                            
            
                                    
            
            

                
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        PRT.write('\n')

            


            
                                                                        
                            
            
                                    
            
            

                
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        for GO in path:

            


            
                                                                        
                            
            
                                    
            
            

                
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            PRT.write('{}\n'.format(GO))

            


            
                                                                                                            
                            
            
                                    
            
            

                
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def chk_results(actual_paths, expected_paths):

            


            
                                                                                                            
                            
            
                                    
            
            

                
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    for actual_path in actual_paths:

            


            
                                                                                                            
                            
            
                                    
            
            

                
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        # GOTerm -> list of Strings

            


            
                                                                                                            
                            
            
                                    
            
            

                
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        actual = [GO.id for GO in actual_path]

            


            
                                                                                                            
                            
            
                                    
            
            

                
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        if actual not in expected_paths:

            


            
                                                                                                            
                            
            
                                    
            
            

                
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            raise Exception('ACTUAL {} NOT FOUND IN EXPECTED RESULTS\n'.format(actual))

            


            
                                                                                                            
                            
            
                                    
            
            

                
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def test_paths_to_top():

            


            
                                                                                                            
                            
            
                                    
            
            

                
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    dag = GODag(ROOT + "mini_obo.obo")

            


            
                                                                                                            
                            
            
                                    
            
            

                
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    expected_paths = [['GO:0000001', 'GO:0000002', 'GO:0000005', 'GO:0000010'],

            


            
                                                                                                            
                            
            
                                    
            
            

                
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                      ['GO:0000001', 'GO:0000003', 'GO:0000005', 'GO:0000010'],

            


            
                                                                                                            
                            
            
                                    
            
            

                
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                      ['GO:0000001', 'GO:0000003', 'GO:0000006', 'GO:0000008', 'GO:0000010']]

            


            
                                                                                                            
                            
            
                                    
            
            

                
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    actual_paths = dag.paths_to_top("GO:0000010")

            


            
                                                                                                            
                                                                
            
                                    
            
            

                
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    chk_results(actual_paths, expected_paths)

            


            
                                                        
            
                                    
            
            

                
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    print_paths(actual_paths)