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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 import itertools
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7
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8 #---------------------------------Arguments------------------------------------------
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9
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10 subprocess.call(['mkdir', 'out'])
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11 parser = argparse.ArgumentParser()
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12
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13 parser.add_argument("-pos", "--positions", help="number of additional nucleotides", action="store")
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14 parser.add_argument("-tool_dir", "--tool_directory", help="tool directory path", action="store")
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15 parser.add_argument("-gen", "--genome", help="genome version", action="store")
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16 parser.add_argument("-gff3", "--gff", help="gff file",action="store")
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17 args = parser.parse_args()
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18
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19 #-----------------------Download and read of the gff3 file---------------------------------
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20
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21 def read_url(q):
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22
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23 url = 'https://mirbase.org/download/CURRENT/genomes/'+args.gff
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24 data = urllib.request.urlopen(url).read()
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25 file_mirna = data.decode('utf-8')
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26 file_mirna = file_mirna.split("\n")
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27 q.put(file_mirna)
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28
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29
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30 #-----------------------Export of the original gff3 file---------------------------------
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31
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32 def write_gff(file_mirna):
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33 f = open('original_mirnas.bed', "w")
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34
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35 for i in range(len(file_mirna)):
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36 f.write(file_mirna[i] + "\n")
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37
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38 #------------------------Process and export of the file with mature mirnas-------------------------------
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39
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40 def new_gff(file_mirna):
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41
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42 mirna = [] # new list with shifted mirnas
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43 positions =int(args.positions) # positions shifted
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44 print(str(positions)+" positions shifted")
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45 names=[]
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46
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47 for i in range(len(file_mirna)):
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48
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49 # Remove lines which conatain the word "primary"
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50 if "primary" not in file_mirna[i]:
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51 mirna.append(file_mirna[i])
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52
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53 # Check if the line starts with "chr"
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54 if "chr" in file_mirna[i]:
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55 a=file_mirna[i].split("\t")[0]
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56 b=file_mirna[i].split("\t")[6]
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57 c=file_mirna[i].split("=")[3].split(";")[0]
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58 names.append([a,b,c])
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59
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60 names.sort()
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61 sublists=[]
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62
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63 [sublists.append([item] * names.count(item)) for item in names if names.count(item)>=2]
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64 sublists.sort()
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65 sublists=list(sublists for sublists, _ in itertools.groupby(sublists))
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66 unique_names=[[x[0][0],x[0][2]] for x in sublists]
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67
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68 for x in unique_names:
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69 flag = 0
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70 for i in range(len(mirna)):
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71
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72 if "chr" in mirna[i] and mirna[i].split("=")[3].split(";")[0]==x[1] and x[0]==mirna[i].split("\t")[0]:
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73 flag+=1
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74 ktr=mirna[i].split(";")[0]+";"+mirna[i].split(";")[1]+";"+mirna[i].split(";")[2]+"-{"+str(flag)+"}"+";"+mirna[i].split(";")[3]
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75 mirna[i]=ktr
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76
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77
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78 f = open('shifted_mirnas.bed', "w")
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79
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80 for i in range(len(mirna)):
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81
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82 if "chr" in mirna[i]:
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83
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84 # change the name of current mirna
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85 mirna_name_1 = mirna[i].split("=")[3]
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86 mirna_name_2 = mirna[i].split("=")[4]
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87 mirna_name_1 = mirna_name_1.split(";")[0]+"_"+mirna_name_2+"_"+mirna[i].split("\t")[0]
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88 mirna[i] = mirna[i].replace("miRNA", mirna_name_1)
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89
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90 # Shift the position of mirna
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91 start = mirna[i].split("\t")[3]
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92 end = mirna[i].split("\t")[4]
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93 shift_start = int(start)-positions # shift the interval to the left
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94 shift_end = int(end)+positions # shift the interval to the right
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95
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96 # Replace the previous intervals with the new
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97 mirna[i] = mirna[i].replace(start, str(shift_start))
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98 mirna[i] = mirna[i].replace(end, str(shift_end))
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99
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100 f.write(mirna[i] + "\n")
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101
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102 f.close()
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103
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104
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105 #------------------------Extract the sequences of the Custom Arms with getfasta tool-------------------------------
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106
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107 def bedtool(genome):
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108 subprocess.call(["bedtools", "getfasta", "-fi", "/cvmfs/data.galaxyproject.org/byhand/"+genome+"/sam_index/"+genome+".fa", "-bed", "shifted_mirnas.bed", "-fo", "new_ref.fa", "-name", "-s"])
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109 #===================================================================================================================================
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110
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111
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112 if __name__=='__main__':
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113
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114 starttime = time.time()
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115 q = Queue()
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116
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117 # Read the original gff3 file
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118 p1 = Process(target=read_url(q))
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119 p1.start()
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120 p1.join()
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121 file_mirna=q.get()
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122
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123 # Export the original gff3 file
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124 p2 = [Process(target=write_gff(file_mirna))]
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125
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126 # Create the new gff3 file
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127 p2.extend([Process(target=new_gff(file_mirna))])
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128 [x.start() for x in p2]
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129 [x.join() for x in p2]
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130
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131 # Extract the sequences of the Custom Arms
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132 p3 = Process(target=bedtool(args.genome))
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133 p3.start()
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134 p3.join()
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135
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136 print('Runtime: {} seconds'.format(round(time.time() - starttime,2)))
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137
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