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comparison armdb_mirbase.py @ 17:150d8995b9aa draft default tip

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author glogobyte
date Mon, 16 Oct 2023 14:27:43 +0000
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16:d9087bba59e1 17:150d8995b9aa
1 import subprocess
2 import argparse
3 import time
4 import urllib.request
5 from multiprocessing import Process, Queue
6 import itertools
7
8 #---------------------------------Arguments------------------------------------------
9
10 subprocess.call(['mkdir', 'out'])
11 parser = argparse.ArgumentParser()
12
13 parser.add_argument("-pos", "--positions", help="number of additional nucleotides", action="store")
14 parser.add_argument("-tool_dir", "--tool_directory", help="tool directory path", action="store")
15 parser.add_argument("-gen", "--genome", help="genome version", action="store")
16 parser.add_argument("-gff3", "--gff", help="gff file",action="store")
17 args = parser.parse_args()
18
19 #-----------------------Download and read of the gff3 file---------------------------------
20
21 def read_url(q):
22
23 url = 'https://mirbase.org/download/'+args.gff
24 data = urllib.request.urlopen(url).read()
25 file_mirna = data.decode('utf-8')
26 file_mirna = file_mirna.split("\n")
27 q.put(file_mirna)
28
29
30 #-----------------------Export of the original gff3 file---------------------------------
31
32 def write_gff(file_mirna):
33 f = open('original_mirnas.bed', "w")
34
35 for i in range(len(file_mirna)):
36 f.write(file_mirna[i] + "\n")
37
38 #------------------------Process and export of the file with mature mirnas-------------------------------
39
40 def new_gff(file_mirna):
41
42 mirna = [] # new list with shifted mirnas
43 positions =int(args.positions) # positions shifted
44 print(str(positions)+" positions shifted")
45 names=[]
46
47 for i in range(len(file_mirna)):
48
49 # Remove lines which conatain the word "primary"
50 if "primary" not in file_mirna[i]:
51 mirna.append(file_mirna[i])
52
53 # Check if the line starts with "chr"
54 if "chr" in file_mirna[i]:
55 a=file_mirna[i].split("\t")[0]
56 b=file_mirna[i].split("\t")[6]
57 c=file_mirna[i].split("=")[3].split(";")[0]
58 names.append([a,b,c])
59
60 names.sort()
61 sublists=[]
62
63 [sublists.append([item] * names.count(item)) for item in names if names.count(item)>=2]
64 sublists.sort()
65 sublists=list(sublists for sublists, _ in itertools.groupby(sublists))
66 unique_names=[[x[0][0],x[0][2]] for x in sublists]
67
68 for x in unique_names:
69 flag = 0
70 for i in range(len(mirna)):
71
72 if "chr" in mirna[i] and mirna[i].split("=")[3].split(";")[0]==x[1] and x[0]==mirna[i].split("\t")[0]:
73 flag+=1
74 ktr=mirna[i].split(";")[0]+";"+mirna[i].split(";")[1]+";"+mirna[i].split(";")[2]+"-{"+str(flag)+"}"+";"+mirna[i].split(";")[3]
75 mirna[i]=ktr
76
77
78 f = open('shifted_mirnas.bed', "w")
79
80 for i in range(len(mirna)):
81
82 if "chr" in mirna[i]:
83
84 # change the name of current mirna
85 mirna_name_1 = mirna[i].split("=")[3]
86 mirna_name_2 = mirna[i].split("=")[4]
87 mirna_name_1 = mirna_name_1.split(";")[0]+"_"+mirna_name_2+"_"+mirna[i].split("\t")[0]
88 mirna[i] = mirna[i].replace("miRNA", mirna_name_1)
89
90 # Shift the position of mirna
91 start = mirna[i].split("\t")[3]
92 end = mirna[i].split("\t")[4]
93 shift_start = int(start)-positions # shift the interval to the left
94 shift_end = int(end)+positions # shift the interval to the right
95
96 # Replace the previous intervals with the new
97 mirna[i] = mirna[i].replace(start, str(shift_start))
98 mirna[i] = mirna[i].replace(end, str(shift_end))
99
100 f.write(mirna[i] + "\n")
101
102 f.close()
103
104
105 #------------------------Extract the sequences of the Custom Arms with getfasta tool-------------------------------
106
107 def bedtool(genome):
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"])
109 #===================================================================================================================================
110
111
112 if __name__=='__main__':
113
114 starttime = time.time()
115 q = Queue()
116
117 # Read the original gff3 file
118 p1 = Process(target=read_url(q))
119 p1.start()
120 p1.join()
121 file_mirna=q.get()
122
123 # Export the original gff3 file
124 p2 = [Process(target=write_gff(file_mirna))]
125
126 # Create the new gff3 file
127 p2.extend([Process(target=new_gff(file_mirna))])
128 [x.start() for x in p2]
129 [x.join() for x in p2]
130
131 # Extract the sequences of the Custom Arms
132 p3 = Process(target=bedtool(args.genome))
133 p3.start()
134 p3.join()
135
136 print('Runtime: {} seconds'.format(round(time.time() - starttime,2)))
137