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1 import subprocess
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2 import argparse
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3 import time
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4 import urllib.request
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5 from multiprocessing import Process, Queue
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6
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7 #--------------------------------------------Arguments-----------------------------------------------
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8 subprocess.call(['mkdir', 'out'])
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9 parser = argparse.ArgumentParser()
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9
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10 parser.add_argument("-pos", "--positions", help="number of additional nucleotides", action="store")
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11 parser.add_argument("-tool_dir", "--tool_directory", help="tool directory path", action="store")
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9
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12 parser.add_argument("-sym", "--symbol", help="organism symbol",action="store")
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13 args = parser.parse_args()
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14
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15 #------------------------------------Read Fasta files from MirGene-----------------------------------
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16
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17 def read_url(path):
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18
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19 data = urllib.request.urlopen(path).read()
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20 data1 = data.decode('utf-8')
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21 data1 = data1.split("\n")
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22 del data1[-1]
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23 q.put(data1)
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24
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25 #-------------------------------------Generation of Custom Arms--------------------------------------
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26
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27 def custom_arms_mirgene(mat_mirna,pri_mirna):
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28 mat_ext=[]
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29 for i in range(0,len(mat_mirna),2):
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30 if args.symbol in mat_mirna[i]:
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31 mat_seq=mat_mirna[i+1]
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32
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33 for j in range(0,len(pri_mirna),2):
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34 if mat_mirna[i].split("_")[0] == pri_mirna[j].split("_")[0]:
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35 temp_ext = pri_mirna[j+1].split(mat_seq)
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36 mat_ext.append([mat_mirna[i],temp_ext[0][-int(args.positions):]+mat_seq+temp_ext[1][0:int(args.positions)]])
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37
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38 print(str(args.positions)+" positions shifted")
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39 return(mat_ext)
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40
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41 #----------------------------------------Export of Fasta files ---------------------------------------
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42
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43 def write_custom_arms(list,name,c):
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44
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45 f = open(name, "w")
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46 for x in list:
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47 if c==1:
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48 f.write(x[0]+'\n')
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49 f.write(x[1]+'\n')
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50 else:
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51 f.write(x+'\n')
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52
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53 #==================================================================================================================================
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54
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55 if __name__=='__main__':
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56
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57 starttime = time.time()
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58 print(args.symbol)
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59 q = Queue()
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60
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61 # Read of all Fasta files
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62 mat_url = 'https://mirgenedb.org/fasta/ALL?mat=1'
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63 p = [Process(target=read_url(mat_url))]
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64 star_url = 'https://mirgenedb.org/fasta/ALL?star=1'
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65 p.extend([Process(target=read_url(star_url))])
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66 pri_url = 'https://mirgenedb.org/static/data/ALL/ALL--pri-30-30.fas'
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67 p.extend([Process(target=read_url(pri_url))])
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68 [x.start() for x in p]
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69 [x.join() for x in p]
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70
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71 mat_mirna=q.get()
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72 star_mirna=q.get()
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73 pri_mirna=q.get()
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74
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75 # Replace U with T in seqeunces
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76 mat_mirna.extend(star_mirna)
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77 for i in range(1,len(mat_mirna),2):
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78 mat_mirna[i]=mat_mirna[i].replace("U","T")
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79
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80 #Generation of Custom Arms
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81 mat_ext=custom_arms_mirgene(mat_mirna,pri_mirna)
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82
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83 #Export of all Fasta files
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84 p1 = [Process(target=write_custom_arms(mat_mirna,"shifted_mirnas.bed",0))]
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85 p1.extend([Process(target=write_custom_arms(pri_mirna,"original_mirnas.bed",0))])
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86 p1.extend([Process(target=write_custom_arms(mat_ext,"new_ref.fa",1))])
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87 [x.start() for x in p1]
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88 [x.join() for x in p1]
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89
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6
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90 print('Runtime: {} seconds'.format(round(time.time() - starttime,2)))
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