Mercurial > repos > glogobyte > isoread
comparison mirgene.py @ 31:23a88a3ec37d draft
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author | glogobyte |
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date | Wed, 20 Oct 2021 16:39:59 +0000 |
parents | d119424f67b6 |
children |
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30:d119424f67b6 | 31:23a88a3ec37d |
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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)) |