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Push — master ( a47e0a...19735b )
by Marcin
04:27
created

chunker.chunks()   A

↳ Parent: chunker

Complexity

Conditions 2

Size

Total Lines 4
Code Lines 3

Duplication

Lines 0
Ratio 0 %

Importance

Changes 0
Metric Value
cc 2
eloc 3
nop 2
dl 0
loc 4
rs 10
c 0
b 0
f 0
1 

            


            
                                                                                                            
                            
            
                                    
            
            

                
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def chunks(l, n):

            


            
                                                                        
                            
            
                                    
            
            

                
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    """Yield successive n-sized chunks from l."""

            


            
                                                                        
                            
            
                                    
            
            

                
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    for i in range(0, len(l), n):

            


            
                                                                        
                            
            
                                    
            
            

                
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        yield l[i:i + n]

            


            
                                                                                                            
                            
            
                                    
            
            

                
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#main

            


            
                                                                                                            
                            
            
                                    
            
            

                
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f = open('pdb_list.txt').read().split()

            


            
                                                                                                            
                            
            
                                    
            
            

                
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# 30 = runs * 10 = 300cores

            


            
                                                                                                            
                            
            
                                    
            
            

                
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no_of_files = int(round(len(f) / 100))

            


            
                                                                                                            
                            
            
                                    
            
            

                
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c = 0

            


            
                                                                                                            
                            
            
                                    
            
            

                
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for i in chunks(f, no_of_files):

            


            
                                                                                                            
                            
            
                                    
            
            

                
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    txt = "echo '" 

            


            
                                                                                                            
                            
            
                                    
            
            

                
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    # -g farna_hires.csv

            


            
                                                                                                            
                            
            
                                    
            
            

                
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    txt += "/home/magnus/mqaprna_env/mqapRNA/main/mqaprna  -o FARNA__hires_" + str(c) + " " + " ".join(i) +"'"

            


            
                                                                                                            
                            
            
                                    
            
            

                
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    txt += " | qsub -N mq" + str(c) + " -V -cwd -pe mpi 1"

            


            
                                                                                                            
                            
            
                                    
            
            

                
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    print txt

            


            
                                                                                                            
                            
            
                                    
            
            

                
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    c += 1

            


            
                                                                                                            
                                                                
            
                                    
            
            

                
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