annotate mirbase.py @ 32:5d232330e81f draft

Uploaded
author glogobyte
date Wed, 20 Oct 2021 16:40:17 +0000
parents 0e7bd3f72c2c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
1 from mirbase_functions import *
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
2 from mirbase_graphs import *
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
3 import time
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
4 from multiprocessing import Process, Queue, Lock, Pool, Manager, Value
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
5 import subprocess
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
6 import argparse
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
7 import sys
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
8
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
9 subprocess.call(['mkdir','-p', 'split1','split2','split3','split4','Counts','Diff/temp_con','Diff/temp_tre','Diff/n_temp_con','Diff/n_temp_tre'])
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
10
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
11 parser = argparse.ArgumentParser()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
12 parser.add_argument("-analysis", "--anal", help="choose type of analysis", action="store")
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
13 parser.add_argument("-con", "--control", help="input fastq file (controls)", nargs='+', default=[])
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
14 parser.add_argument("-tre", "--treated", help="input fastq file (treated)", nargs='+', default=[] )
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
15 parser.add_argument("-tool_dir", "--tool_directory", help="tool directory path", action="store")
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
16 parser.add_argument("-gen", "--org_name", help="Organism", action="store")
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
17 parser.add_argument("-f", "--flag", help="choose the database (MirBase,MirGene)", action="store")
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
18 parser.add_argument("-percentage", "--per", help="Percentage of Samples", action="store")
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
19 parser.add_argument("-counts", "--count", help="Counts for filtering", action="store")
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
20 parser.add_argument("-name1", "--group1", help="Samples group 1", action="store")
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
21 parser.add_argument("-name2", "--group2", help="Samples group 2", action="store")
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
22 args = parser.parse_args()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
23
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
24
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
25 #################################################################################################################################################################################################################
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
26
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
27 if __name__ == '__main__':
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
28
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
29 starttime = time.time()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
30
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
31 lock = Lock()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
32 manager = Manager()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
33
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
34 # Download reference miRNA sequences from MirBase
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
35 mature_mirnas=manager.list()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
36 ps_mature=Process(target=download_matures,args=(mature_mirnas,args.org_name))
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
37 ps_mature.start()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
38
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
39
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
40 # Keep the names of the files and location paths
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
41 args.control[0]=args.control[0][1:]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
42 args.control[len(args.control)-1][:-1]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
43 control = [(args.control[i:i+2]) for i in range(0, len(args.control), 2)]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
44
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
45
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
46 args.treated[0]=args.treated[0][1:]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
47 args.treated[len(args.treated)-1][:-1]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
48 treated = [(args.treated[i:i+2]) for i in range(0, len(args.treated), 2)]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
49
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
50
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
51 ############## Detection of templated isoforms ################
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
52
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
53
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
54 # Initialization of the managers between the proccesses
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
55 # First group of samples (controls)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
56 con_samples = manager.list() # Collapsed mirnas with the new names
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
57 con_data= manager.list() # keeps all necessary data for the Database
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
58 con_file_order=manager.list() # files' names ordered by processes
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
59 con_names_seqs=manager.list() # keeps only mirna names and sequences
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
60 deseq=manager.list()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
61 con_unmap_seq=manager.Value('i',0) # keeps unmap unique sequnces for the generation of a graph
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
62 con_unmap_counts=manager.Value('i',0) # keeps unmap counts of sequnces for the generation of a graph
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
63 con_mirna_names=manager.list() # keeps the names of mirnas
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
64 ini_con_samples = manager.list() # filtered SAM files
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
65
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
66 # Second group of samples (treated)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
67 tre_samples = manager.list()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
68 tre_data = manager.list()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
69 tre_file_order = manager.list()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
70 tre_names_seqs=manager.list()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
71 deseq1=manager.list()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
72 tre_unmap_seq = manager.Value('i',0)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
73 tre_unmap_counts = manager.Value('i',0)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
74 tre_mirna_names=manager.list()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
75 ini_tre_samples = manager.list()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
76
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
77 # Wait for the download of reference miRNA sequences
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
78 ps_mature.join()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
79 mature_mirnas=list(mature_mirnas)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
80
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
81 # Processing of the detected miRNAs from SAM files
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
82 ps_sam = [Process(target=sam_edit,args=(mature_mirnas,path[1][:-1],path[0].split(",")[0],"c",lock,con_samples,con_data,con_file_order,con_unmap_seq,con_names_seqs,deseq,con_mirna_names,ini_con_samples,con_unmap_counts)) for path in control]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
83 ps_sam.extend([Process(target=sam_edit,args=(mature_mirnas,path[1][:-1],path[0].split(",")[0],"t",lock,tre_samples,tre_data,tre_file_order,tre_unmap_seq,tre_names_seqs,deseq1,tre_mirna_names,ini_tre_samples,tre_unmap_counts)) for path in treated])
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
84
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
85 # Wait for processing of SAM files to finish
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
86 [p.start() for p in ps_sam]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
87 [p.join() for p in ps_sam]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
88
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
89 # Generate a histogram
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
90 ps_hist=[Process(target=hist_red,args=(ini_con_samples,'c',args.group1))]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
91 ps_hist.extend([Process(target=hist_red,args=(ini_tre_samples,'t',args.group2))])
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
92 [x.start() for x in ps_hist]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
93
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
94
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
95 # Convert managers to lists
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
96 con_samples = list(con_samples)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
97 tre_samples = list(tre_samples)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
98 con_file_order=list(con_file_order)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
99 tre_file_order=list(tre_file_order)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
100 deseq=list(deseq)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
101 deseq1=list(deseq1)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
102
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
103 # Remove duplicates and sorting
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
104 con_names_seqs=list(con_names_seqs)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
105 con_names_seqs.sort()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
106 con_names_seqs=list(con_names_seqs for con_names_seqs,_ in itertools.groupby(con_names_seqs))
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
107
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
108 tre_names_seqs=list(tre_names_seqs)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
109 tre_names_seqs.sort()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
110 tre_names_seqs=list(tre_names_seqs for tre_names_seqs,_ in itertools.groupby(tre_names_seqs))
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
111
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
112 # initialization of new managers
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
113 new_con_file_order=manager.list()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
114 new_tre_file_order=manager.list()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
115 new_deseq=manager.list()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
116 new_deseq1=manager.list()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
117
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
118 # add uncommon detected mirnas among the samples
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
119 ps_un_mirnas=[Process(target=uncommon_mirnas,args=(sampp,con_names_seqs,lock,new_deseq,con_file_order[i],new_con_file_order)) for i,sampp in enumerate(deseq)]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
120 ps_un_mirnas.extend([Process(target=uncommon_mirnas,args=(sampp,tre_names_seqs,lock,new_deseq1,tre_file_order[i],new_tre_file_order)) for i,sampp in enumerate(deseq1)])
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
121
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
122 # Wait for processing of uncommon detected mirnas to finish
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
123 [z.start() for z in ps_un_mirnas]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
124 [z.join() for z in ps_un_mirnas]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
125
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
126 # Convert managers to lists
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
127 new_deseq=list(new_deseq)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
128 new_deseq1=list(new_deseq1)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
129 con_file_order=list(new_con_file_order)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
130 tre_file_order=list(new_tre_file_order)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
131
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
132 # Genereation of count matrices per group (controls - treated)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
133 control_group=[[x[0],x[2]] for x in new_deseq[0]]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
134 [control_group[i].append(y[i][1]) for i,_ in enumerate(control_group) for y in new_deseq]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
135
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
136 treated_group=[[x[0],x[2]] for x in new_deseq1[0]]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
137 [treated_group[i].append(y[i][1]) for i,_ in enumerate(treated_group) for y in new_deseq1]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
138
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
139 # Keep a copy of count matrices
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
140 control_group_copy=copy.deepcopy(list(control_group))
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
141 treated_group_copy=copy.deepcopy(list(treated_group))
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
142
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
143 # Initialization of managers
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
144 merg_nam_control_group=manager.list()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
145 merg_nam_treated_group=manager.list()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
146
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
147 # Merging of names different names for the same mirna sequence per group (controls, treated) to avoid duplicates
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
148 ps_merge = [Process(target=merging_names,args=(control_group_copy,merg_nam_control_group))]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
149 ps_merge.extend([Process(target=merging_names,args=(treated_group_copy,merg_nam_treated_group))])
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
150 [x.start() for x in ps_merge]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
151
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
152
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
153 # Add unique mirna sequences between groups (all groups will have the same amount of sequences)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
154 con_list=manager.list()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
155 tre_list=manager.list()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
156
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
157 ps_bw = [Process(target=black_white,args=(con_names_seqs,tre_names_seqs,treated_group,tre_list))]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
158 ps_bw.extend([Process(target=black_white,args=(tre_names_seqs,con_names_seqs,control_group,con_list))])
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
159 [x.start() for x in ps_bw]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
160 [x.join() for x in ps_bw]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
161
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
162 control_group=list(con_list)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
163 treated_group=list(tre_list)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
164
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
165 # Detection of duplications
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
166 dupes=manager.list()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
167
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
168 ps_dupes = Process(target=merging_dupes,args=(control_group,dupes))
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
169 ps_dupes.start()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
170 ps_dupes.join()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
171
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
172 dupes=list(dupes)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
173
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
174 # Merging the duplications in one entry with all different names
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
175 con_list=manager.list()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
176 tre_list=manager.list()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
177
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
178 ps_ap_merg_dupes = [Process(target=apply_merging_dupes,args=(control_group,dupes,con_list))]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
179 ps_ap_merg_dupes.extend([Process(target=apply_merging_dupes,args=(treated_group,dupes,tre_list))])
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
180 [x.start() for x in ps_ap_merg_dupes]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
181
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
182 # Preparation of reference sequences (isodforms) for the detection of non template mirnas
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
183 if args.anal=="2":
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
184 all_iso = manager.list()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
185 ps_non_iso = Process(target=non_template_ref,args=(con_samples,tre_samples,all_iso))
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
186 ps_non_iso.start()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
187
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
188 # Finishing the process for merging
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
189 [x.join() for x in ps_merge]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
190 merg_nam_control_group=list(merg_nam_control_group)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
191 merg_nam_treated_group=list(merg_nam_treated_group)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
192
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
193 # Export the database and the graphs
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
194 procs = [Process(target=DB_write,args=(x[0],x[1],x[2],x[3],1)) for x in con_data]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
195 procs.extend([Process(target=DB_write,args=(x[0],x[1],x[2],x[3],1)) for x in tre_data])
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
196 procs.extend([Process(target=make_spider,args=(merg_nam_control_group,merg_nam_treated_group,args.group1,args.group2))])
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
197
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
198 if args.anal == "1":
23
6d3abc45aa49 Uploaded
glogobyte
parents: 1
diff changeset
199 procs.extend([Process(target=pie_temp,args=(merg_nam_control_group,con_unmap_seq.value,con_unmap_counts.value,merg_nam_treated_group,tre_unmap_seq.value,tre_unmap_counts.value,args.group1,args.group2))])
1
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
200
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
201 [p.start() for p in procs]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
202
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
203 # Export the pdf report file
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
204 if args.anal=="1":
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
205 [x.join() for x in ps_hist]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
206 [p.join() for p in procs]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
207 ps_pdf = Process(target=pdf_before_DE,args=(args.anal,args.group1,args.group2))
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
208 ps_pdf.start()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
209
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
210
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
211 [x.join() for x in ps_ap_merg_dupes]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
212 control_group=list(con_list)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
213 treated_group=list(tre_list)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
214
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
215 # Filters low count mirnas (otpional)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
216 if int(args.per)!=-1:
32
5d232330e81f Uploaded
glogobyte
parents: 29
diff changeset
217 if int(args.per)>0 and int(args.per)<=100 and int(args.count)>0:
1
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
218
29
0e7bd3f72c2c Uploaded
glogobyte
parents: 27
diff changeset
219 fil_con_group=manager.list()
0e7bd3f72c2c Uploaded
glogobyte
parents: 27
diff changeset
220 fil_tre_group=manager.list()
1
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
221
29
0e7bd3f72c2c Uploaded
glogobyte
parents: 27
diff changeset
222 ps_low_counts = Process(target=filter_low_counts,args=(control_group,treated_group,fil_con_group,fil_tre_group,args.per,args.count))
0e7bd3f72c2c Uploaded
glogobyte
parents: 27
diff changeset
223 ps_low_counts.start()
0e7bd3f72c2c Uploaded
glogobyte
parents: 27
diff changeset
224 ps_low_counts.join()
1
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
225
29
0e7bd3f72c2c Uploaded
glogobyte
parents: 27
diff changeset
226 fil_con_group=list(fil_con_group)
0e7bd3f72c2c Uploaded
glogobyte
parents: 27
diff changeset
227 fil_tre_group=list(fil_tre_group)
0e7bd3f72c2c Uploaded
glogobyte
parents: 27
diff changeset
228 else:
0e7bd3f72c2c Uploaded
glogobyte
parents: 27
diff changeset
229 sys.exit("Not acceptable values for filter")
0e7bd3f72c2c Uploaded
glogobyte
parents: 27
diff changeset
230
1
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
231
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
232 if "fil_con_group" not in locals() or "fil_con_group" not in globals():
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
233 fil_con_group=control_group
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
234 fil_tre_group=treated_group
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
235
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
236 # export count matrices
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
237 ps_write = Process(target=write_main,args=(control_group, treated_group, fil_con_group, fil_tre_group, con_file_order,tre_file_order,1,args.group1,args.group2,args.per))
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
238 ps_write.start()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
239
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
240 # export counts files compatible with Deseq2 and EdgeR
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
241 ps1_matrix = [Process(target=temp_counts_to_diff,args=(con_file_order,fil_con_group,"Diff/temp_con/"))]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
242 ps1_matrix.extend([Process(target=temp_counts_to_diff,args=(tre_file_order,fil_tre_group,"Diff/temp_tre/"))])
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
243 [p.start() for p in ps1_matrix]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
244
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
245 if args.anal=="1":
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
246 ps_pdf.join()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
247 if args.anal=="2":
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
248 [p.join() for p in procs]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
249 [x.join() for x in ps_hist]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
250
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
251 ps_write.join()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
252 [p.join() for p in ps1_matrix]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
253
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
254 ############################## Detection of non-template #######################################
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
255
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
256 if args.anal == "2":
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
257
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
258 # Initialization of the managers between the proccesses
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
259 # First group of samples (controls)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
260 n_con_data= manager.list()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
261 n_con_file_order=manager.list()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
262 n_con_names_seqs=manager.list()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
263 n_deseq=manager.list()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
264
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
265 # Second group of samples (treated)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
266 n_tre_data = manager.list()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
267 n_tre_file_order = manager.list()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
268 n_tre_names_seqs=manager.list()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
269 n_deseq1=manager.list()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
270
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
271 # Preparation of reference sequences
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
272 new_ref_mirnas = list(mature_mirnas)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
273 ps_non_iso.join()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
274
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
275 all_iso=list(all_iso)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
276 new_ref_mirnas.extend(all_iso)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
277
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
278 # Processing of non template miRNAs from SAM files
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
279 ps_sam = [Process(target=non_sam_edit,args=(new_ref_mirnas,path[1][:-1],path[0].split(",")[0],"c",lock,n_con_data,n_con_file_order,n_deseq,n_con_names_seqs)) for path in control]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
280 ps_sam.extend([Process(target=non_sam_edit,args=(new_ref_mirnas,path[1][:-1],path[0].split(",")[0],"t",lock,n_tre_data,n_tre_file_order,n_deseq1,n_tre_names_seqs)) for path in treated])
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
281
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
282 [p.start() for p in ps_sam]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
283 [p.join() for p in ps_sam]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
284
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
285 # Convert managers to lists
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
286 n_con_file_order=list(n_con_file_order)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
287 n_tre_file_order=list(n_tre_file_order)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
288 n_deseq=list(n_deseq)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
289 n_deseq1=list(n_deseq1)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
290
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
291 # Remove duplicates and sorting
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
292 n_con_names_seqs=list(n_con_names_seqs)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
293 n_con_names_seqs.sort()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
294 n_con_names_seqs=list(n_con_names_seqs for n_con_names_seqs,_ in itertools.groupby(n_con_names_seqs))
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
295
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
296 n_tre_names_seqs=list(n_tre_names_seqs)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
297 n_tre_names_seqs.sort()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
298 n_tre_names_seqs=list(n_tre_names_seqs for n_tre_names_seqs,_ in itertools.groupby(n_tre_names_seqs))
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
299
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
300 # initialization of new managers
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
301 new_n_con_file_order=manager.list()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
302 new_n_tre_file_order=manager.list()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
303 n_new_deseq=manager.list()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
304 n_new_deseq1=manager.list()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
305
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
306 # add uncommon detected mirnas among the samples
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
307 ps_deseq=[Process(target=uncommon_mirnas,args=(sampp,n_con_names_seqs,lock,n_new_deseq,n_con_file_order[i],new_n_con_file_order)) for i,sampp in enumerate(n_deseq)]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
308 ps_deseq.extend([Process(target=uncommon_mirnas,args=(sampp,n_tre_names_seqs,lock,n_new_deseq1,n_tre_file_order[i],new_n_tre_file_order)) for i,sampp in enumerate(n_deseq1)])
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
309
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
310 # Wait for processing of uncommon detected mirnas to finish
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
311 [x.start() for x in ps_deseq]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
312 [x.join() for x in ps_deseq]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
313
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
314 # Convert managers to lists
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
315 n_new_deseq=list(n_new_deseq)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
316 n_new_deseq1=list(n_new_deseq1)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
317 n_con_file_order=list(new_n_con_file_order)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
318 n_tre_file_order=list(new_n_tre_file_order)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
319
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
320 # Genereation of count matrices per group (controls - treated)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
321 n_control_group=[[x[0],x[2]] for x in n_new_deseq[0]]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
322 [n_control_group[i].append(y[i][1]) for i,_ in enumerate(n_control_group) for y in n_new_deseq]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
323
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
324 n_treated_group=[[x[0],x[2]] for x in n_new_deseq1[0]]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
325 [n_treated_group[i].append(y[i][1]) for i,_ in enumerate(n_treated_group) for y in n_new_deseq1]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
326
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
327 # Keep a copy of count matrices
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
328 n_control_group_copy=copy.deepcopy(list(n_control_group))
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
329 n_treated_group_copy=copy.deepcopy(list(n_treated_group))
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
330
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
331 # Initialization of managers
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
332 merg_nam_n_control_group=manager.list()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
333 merg_nam_n_treated_group=manager.list()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
334
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
335 # Merging of names different names for the same mirna sequence per group (controls, treated) to avoid duplicates\
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
336 ps_merge = [Process(target=merging_names,args=(n_control_group_copy,merg_nam_n_control_group))]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
337 ps_merge.extend([Process(target=merging_names,args=(n_treated_group_copy,merg_nam_n_treated_group))])
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
338 [x.start() for x in ps_merge]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
339
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
340 # Add unique mirna sequences between groups (all groups will have the same amount of sequences)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
341 n_con_list=manager.list()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
342 n_tre_list=manager.list()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
343
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
344 ps_bw = [Process(target=black_white,args=(n_con_names_seqs,n_tre_names_seqs,n_treated_group,n_tre_list))]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
345 ps_bw.extend([Process(target=black_white,args=(n_tre_names_seqs,n_con_names_seqs,n_control_group,n_con_list))])
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
346 [x.start() for x in ps_bw]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
347 [x.join() for x in ps_bw]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
348
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
349 n_control_group=list(n_con_list)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
350 n_treated_group=list(n_tre_list)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
351
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
352 # Detection of duplications
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
353 n_dupes=manager.list()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
354
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
355 ps_dupes = Process(target=merging_dupes,args=(n_control_group,n_dupes))
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
356 ps_dupes.start()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
357 ps_dupes.join()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
358
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
359 n_dupes=list(n_dupes)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
360
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
361 # Merging the duplications in one entry with all different names
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
362 n_con_list=manager.list()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
363 n_tre_list=manager.list()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
364
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
365 ps_ap_merg_dupes = [Process(target=apply_merging_dupes,args=(n_control_group,n_dupes,n_con_list))]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
366 ps_ap_merg_dupes.extend([Process(target=apply_merging_dupes,args=(n_treated_group,n_dupes,n_tre_list))])
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
367 [x.start() for x in ps_ap_merg_dupes]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
368
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
369 # Finishing the process for merging
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
370 [x.join() for x in ps_merge]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
371 merg_nam_n_control_group=list(merg_nam_n_control_group)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
372 merg_nam_n_treated_group=list(merg_nam_n_treated_group)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
373
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
374 # Export the database and the graphs
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
375 procs = [Process(target=DB_write,args=(x[0],x[1],x[2],x[3],2)) for x in n_con_data]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
376 procs.extend([Process(target=DB_write,args=(x[0],x[1],x[2],x[3],2)) for x in n_tre_data])
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
377 procs.extend([Process(target=logo_seq_red,args=(merg_nam_n_control_group,'c',args.group1))])
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
378 procs.extend([Process(target=logo_seq_red,args=(merg_nam_n_treated_group,'t',args.group2))])
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
379 procs.extend([Process(target=pie_non_temp,args=(merg_nam_control_group,merg_nam_n_control_group,merg_nam_treated_group,merg_nam_n_treated_group,con_unmap_seq.value,tre_unmap_seq.value,con_unmap_counts.value,tre_unmap_counts.value,args.group1,args.group2))])
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
380
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
381 [p.start() for p in procs]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
382 [p.join() for p in procs]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
383
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
384 procs1 = Process(target=pdf_before_DE,args=(args.anal,args.group1,args.group2))
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
385 procs1.start()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
386
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
387 [x.join() for x in ps_ap_merg_dupes]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
388 n_control_group=list(n_con_list)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
389 n_treated_group=list(n_tre_list)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
390
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
391
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
392 # Filters low count mirnas (otpional)
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
393 if int(args.per)!=-1:
32
5d232330e81f Uploaded
glogobyte
parents: 29
diff changeset
394 if int(args.per)>0 and int(args.per)<=100 and int(args.count)>0:
1
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
395
29
0e7bd3f72c2c Uploaded
glogobyte
parents: 27
diff changeset
396 n_fil_con_group=manager.list()
0e7bd3f72c2c Uploaded
glogobyte
parents: 27
diff changeset
397 n_fil_tre_group=manager.list()
1
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
398
29
0e7bd3f72c2c Uploaded
glogobyte
parents: 27
diff changeset
399 ps_low_counts = Process(target=filter_low_counts,args=(n_control_group,n_treated_group,n_fil_con_group,n_fil_tre_group,args.per,args.count))
0e7bd3f72c2c Uploaded
glogobyte
parents: 27
diff changeset
400 ps_low_counts.start()
0e7bd3f72c2c Uploaded
glogobyte
parents: 27
diff changeset
401 ps_low_counts.join()
1
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
402
29
0e7bd3f72c2c Uploaded
glogobyte
parents: 27
diff changeset
403 n_fil_con_group=list(n_fil_con_group)
0e7bd3f72c2c Uploaded
glogobyte
parents: 27
diff changeset
404 n_fil_tre_group=list(n_fil_tre_group)
0e7bd3f72c2c Uploaded
glogobyte
parents: 27
diff changeset
405
0e7bd3f72c2c Uploaded
glogobyte
parents: 27
diff changeset
406 else:
0e7bd3f72c2c Uploaded
glogobyte
parents: 27
diff changeset
407 sys.exit("Not acceptable values for filter")
0e7bd3f72c2c Uploaded
glogobyte
parents: 27
diff changeset
408
1
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
409 if "n_fil_con_group" not in locals() or "n_fil_con_group" not in globals():
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
410 n_fil_con_group=n_control_group
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
411 n_fil_tre_group=n_treated_group
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
412
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
413 ps_write = Process(target=write_main,args=(n_control_group, n_treated_group,n_fil_con_group, n_fil_tre_group, n_con_file_order, n_tre_file_order,2,args.group1,args.group2,args.per))
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
414 ps_write.start()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
415
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
416 ps1_matrix = [Process(target=nontemp_counts_to_diff,args=(n_con_file_order,n_fil_con_group,con_file_order,fil_con_group,"Diff/n_temp_con/"))]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
417 ps1_matrix.extend([Process(target=nontemp_counts_to_diff,args=(n_tre_file_order,n_fil_tre_group,tre_file_order,fil_tre_group,"Diff/n_temp_tre/"))])
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
418 [p.start() for p in ps1_matrix]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
419
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
420 ps_write.join()
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
421 [p.join() for p in ps1_matrix]
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
422 procs1.join()
27
6e365f2eb24a Uploaded
glogobyte
parents: 23
diff changeset
423 print('Running time: {} seconds'.format(round(time.time() - starttime,2)))
1
f10c8f43f010 Uploaded
glogobyte
parents:
diff changeset
424