Mercurial > repos > glogobyte > mirviz

comparison viz.py @ 5:4d59ac081282 draft

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author glogobyte
date Wed, 13 Oct 2021 11:19:17 +0000
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children 0a4d6c483ff0
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4:216888953a0a 5:4d59ac081282
1 from viz_graphs import *
2 from viz_functions import *
3 import argparse
4 import time
5 from multiprocessing import Process, Lock, Manager
6
7 ##################################################################################################################################################################################################################################################################
8 starttime = time.time()
9
10 parser = argparse.ArgumentParser()
11 parser.add_argument("-in", "--input", help="choose type of analysis", action="store")
12 parser.add_argument("-p_value", "--pval", help="choose type of analysis", action="store")
13 parser.add_argument("-fc", "--log2fc", help="choose type of analysis", action="store")
14 parser.add_argument("-top", "--top_mirnas", help="choose type of analysis", action="store")
15 parser.add_argument("-tool_dir", "--tool_directory", help="tool directory path", action="store")
16 parser.add_argument("-statistic", "--stat", help="tool directory path", action="store")
17 parser.add_argument("-diff_tool", "--tool", help="tool directory path", action="store")
18
19 args = parser.parse_args()
20
21 l=Lock()
22 number = int(args.top_mirnas)
23 log2fc = float(args.log2fc)
24 pval = float(args.pval)
25 iso_star_flag=0
26 non_star_flag=0
27
28 if args.tool=="2":
29
30 raw_EdgeR = read(args.input,0)
31 EdgeR = [x.rstrip("\n").split("\t") for x in raw_EdgeR]
32 del EdgeR[0]
33 for x in EdgeR:
34 if "/" in x[0]:
35 x[0]=x[0].split("/")[0]+"★"
36
37 if args.stat=="1":
38 non_templated = [[x[0],x[1],x[4]] for x in EdgeR if "nt" in x[0] and x[1]!="NA" and x[4]!="NA"]
39 matures = [[x[0],x[1],x[4]] for x in EdgeR if 'chr' in x[0].split("_")[-1] and "nt" not in x[0] and x[1]!="NA" and x[4]!="NA"]
40 isoforms = [[x[0],x[1],x[4]] for x in EdgeR if 'chr' not in x[0].split("_")[-1] and "nt" not in x[0] and x[1]!="NA" and x[4]!="NA"]
41 else:
42 non_templated = [[x[0],x[1],x[5]] for x in EdgeR if "nt" in x[0] and x[1]!="NA" and x[5]!="NA"]
43 matures = [[x[0],x[1],x[5]] for x in EdgeR if 'chr' in x[0].split("_")[-1] and "nt" not in x[0] and x[1]!="NA" and x[5]!="NA"]
44 isoforms = [[x[0],x[1],x[5]] for x in EdgeR if 'chr' not in x[0].split("_")[-1] and "nt" not in x[0] and x[1]!="NA" and x[5]!="NA"]
45
46 if args.tool=="1":
47
48 raw_Deseq = read(args.input,0)
49 Deseq = [x.rstrip("\n").split("\t") for x in raw_Deseq]
50 for x in Deseq:
51 if "/" in x[0]:
52 x[0]=x[0].split("/")[0]+"★"
53
54 if args.stat=="1":
55 non_templated = [[x[0],x[2],x[5]] for x in Deseq if "nt" in x[0] and x[2]!="NA" and x[5]!="NA"]
56 matures = [[x[0],x[2],x[5]] for x in Deseq if 'chr' in x[0].split("_")[-1] and "nt" not in x[0] and x[2]!="NA" and x[5]!="NA"]
57 isoforms = [[x[0],x[2],x[5]] for x in Deseq if 'chr' not in x[0].split("_")[-1] and "nt" not in x[0] and x[2]!="NA" and x[5]!="NA"]
58 elif args.stat=="2":
59 non_templated = [[x[0],x[2],x[6]] for x in Deseq if "nt" in x[0] and x[2]!="NA" and x[6]!="NA"]
60 matures = [[x[0],x[2],x[6]] for x in Deseq if 'chr' in x[0].split("_")[-1] and "nt" not in x[0] and x[2]!="NA" and x[6]!="NA"]
61 isoforms = [[x[0],x[2],x[6]] for x in Deseq if 'chr' not in x[0].split("_")[-1] and "nt" not in x[0] and x[2]!="NA" and x[6]!="NA"]
62 else:
63 non_templated = [[x[0],x[2],x[1]] for x in Deseq if "nt" in x[0] and x[2]!="NA" and x[1]!="NA"]
64 matures = [[x[0],x[2],x[1]] for x in Deseq if 'chr' in x[0].split("_")[-1] and "nt" not in x[0] and x[2]!="NA" and x[1]!="NA"]
65 isoforms = [[x[0],x[2],x[1]] for x in Deseq if 'chr' not in x[0].split("_")[-1] and "nt" not in x[0] and x[2]!="NA" and x[1]!="NA"]
66
67
68 diff_matures,diff_isoforms,diff_non_templated,names,non_temp,mat_iso = preproccess(non_templated,matures,isoforms,log2fc,pval,args.stat)
69 for x in mat_iso[:number]:
70 if "★" in x[0]:
71 iso_star_flag=1
72 break
73 for x in non_temp[:number]:
74 if "★" in x[0]:
75 non_star_flag=1
76 break
77
78
79 if non_templated!=[]:
80 analysis="2"
81 p=[Process(target=top_diff,args=(non_temp,number,"nt",l))]
82 p.extend([Process(target=top_diff,args=(mat_iso,number,"t",l))])
83 p.extend([Process(target=top_scatter_non,args=(diff_matures,diff_isoforms,diff_non_templated,names,number))])
84
85 else:
86 analysis="1"
87 p=[Process(target=top_diff,args=(mat_iso,number,"t",l))]
88 p.extend([Process(target=top_scatter_tem,args=(diff_matures,diff_isoforms,names,number))])
89
90 [x.start() for x in p]
91 [x.join() for x in p]
92
93 pdf_after_DE(analysis,args.top_mirnas,args.tool_directory,iso_star_flag,non_star_flag)
94
95 print('That took {} seconds'.format(time.time() - starttime))
96