View GitHub Repository rna-tools

Schedule Inspection
Subscribe
Passed
Push — master ( a47e0a...19735b )
by Marcin
04:27
created

chunker   A

↳ Parent: Project

Complexity

Total Complexity 2

Size/Duplication

Total Lines 21
Duplicated Lines 0 %

Importance

Changes 0
Metric Value
eloc 13
dl 0
loc 21
rs 10
c 0
b 0
f 0
wmc 2

1 Function

Rating   Name   Duplication   Size   Complexity  
A chunks() 0 4 2
1 

            


            
                                                        
            
                                    
            
            

                
                    2
                

                                    
                                                    
                
                
                

            


            
                                                        
            
                                    
            
            

                
                    3
                

                                    
                                                    
                
                
                

            


            
                                                        
            
                                    
            
            

                
                    4
                

                                    
                                                    
                
                
                
def chunks(l, n):

            


            
                                                        
            
                                    
            
            

                
                    5
                

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

            


            
                                                        
            
                                    
            
            

                
                    6
                

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

            


            
                                                        
            
                                    
            
            

                
                    7
                

                                    
                                                    
                
                
                
        yield l[i:i + n]

            


            
                                                        
            
                                    
            
            

                
                    8
                

                                    
                                                    
                
                
                

            


            
                                                        
            
                                    
            
            

                
                    9
                

                                    
                                                    
                
                
                
#main

            


            
                                                        
            
                                    
            
            

                
                    10
                

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

            


            
                                                        
            
                                    
            
            

                
                    11
                

                                    
                                                    
                
                
                
# 30 = runs * 10 = 300cores

            


            
                                                        
            
                                    
            
            

                
                    12
                

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

            


            
                                                        
            
                                    
            
            

                
                    13
                

                                    
                                                    
                
                
                
c = 0

            


            
                                                        
            
                                    
            
            

                
                    14
                

                                    
                                                    
                
                
                
for i in chunks(f, no_of_files):

            


            
                                                        
            
                                    
            
            

                
                    15
                

                                    
                                                    
                
                
                
    txt = "echo '" 

            


            
                                                        
            
                                    
            
            

                
                    16
                

                                    
                                                    
                
                
                
    # -g farna_hires.csv

            


            
                                                        
            
                                    
            
            

                
                    17
                

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

            


            
                                                        
            
                                    
            
            

                
                    18
                

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

            


            
                                                        
            
                                    
            
            

                
                    19
                

                                    
                                                    
                
                
                
    print txt

            


            
                                                        
            
                                    
            
            

                
                    20
                

                                    
                                                    
                
                
                
    c += 1

            


            
                                                        
            
                                    
            
            

                
                    21
                

                                    
                                                    
                
                
                
    

            


            
                                                        
            
                                    
            
            

                
                    22