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comparison mirgene.py @ 31:23a88a3ec37d draft

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author glogobyte
date Wed, 20 Oct 2021 16:39:59 +0000
parents d119424f67b6
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30:d119424f67b6 31:23a88a3ec37d
2 from mirgene_graphs import * 2 from mirgene_graphs import *
3 import time 3 import time
4 from multiprocessing import Process, Queue, Lock, Pool, Manager, Value 4 from multiprocessing import Process, Queue, Lock, Pool, Manager, Value
5 import subprocess 5 import subprocess
6 import argparse 6 import argparse
7 import sys
7 8
8 subprocess.call(['mkdir','-p','split1','split2','split3','split4','Counts','Diff/temp_con','Diff/temp_tre','Diff/n_temp_con','Diff/n_temp_tre']) 9 subprocess.call(['mkdir','-p','split1','split2','split3','split4','Counts','Diff/temp_con','Diff/temp_tre','Diff/n_temp_con','Diff/n_temp_tre'])
9 10
10 parser = argparse.ArgumentParser() 11 parser = argparse.ArgumentParser()
11 parser.add_argument("-analysis", "--anal", help="choose type of analysis", action="store") 12 parser.add_argument("-analysis", "--anal", help="choose type of analysis", action="store")
204 control_group=list(con_list) 205 control_group=list(con_list)
205 treated_group=list(tre_list) 206 treated_group=list(tre_list)
206 207
207 # Filters low count mirnas (otpional) 208 # Filters low count mirnas (otpional)
208 if int(args.per)!=-1: 209 if int(args.per)!=-1:
209 if int(args.per)>0 and float(args.per)<=100 and int(args.count)>0: 210 if int(args.per)>0 and int(args.per)<=100 and int(args.count)>0:
210 fil_con_group=manager.list() 211 fil_con_group=manager.list()
211 fil_tre_group=manager.list() 212 fil_tre_group=manager.list()
212 213
213 ps_low_counts = Process(target=filter_low_counts,args=(control_group,treated_group,fil_con_group,fil_tre_group,args.per,args.count)) 214 ps_low_counts = Process(target=filter_low_counts,args=(control_group,treated_group,fil_con_group,fil_tre_group,args.per,args.count))
214 ps_low_counts.start() 215 ps_low_counts.start()
380 n_control_group=list(n_con_list) 381 n_control_group=list(n_con_list)
381 n_treated_group=list(n_tre_list) 382 n_treated_group=list(n_tre_list)
382 383
383 # Filters low count mirnas (otpional) 384 # Filters low count mirnas (otpional)
384 if int(args.per)!=-1: 385 if int(args.per)!=-1:
385 if int(args.per)>0 and float(args.per)<=100 and int(args.count)>0: 386 if int(args.per)>0 and int(args.per)<=100 and int(args.count)>0:
386 387
387 n_fil_con_group=manager.list() 388 n_fil_con_group=manager.list()
388 n_fil_tre_group=manager.list() 389 n_fil_tre_group=manager.list()
389 390
390 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)) 391 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))