Mercurial > repos > glogobyte > isoread

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mirbase_ultra_v2.py	Thu Oct 22 08:16:01 2020 +0000
@@ -0,0 +1,367 @@
+from mirbase_functions import *
+from mirbase_graphs import *
+import itertools
+import time
+import sys
+import os
+import urllib.request
+import gzip
+from multiprocessing import Process, Queue, Lock, Pool, Manager, Value
+import subprocess
+import argparse
+from collections import OrderedDict
+from matplotlib.backends.backend_pdf import PdfPages
+import pandas as pd
+from math import pi
+import numpy as np
+import matplotlib.pyplot as plt
+from matplotlib.ticker import PercentFormatter
+import seaborn as sns
+import scipy.stats as stats
+from plotnine import *
+import math
+import re
+import matplotlib.ticker as mtick
+import copy
+
+subprocess.call(['mkdir','-p', 'split1','split2','split3','split4','split11','split12','Counts','Diff/temp_con','Diff/temp_tre','Diff/n_temp_con','Diff/n_temp_tre'])
+
+parser = argparse.ArgumentParser()
+parser.add_argument("-analysis", "--anal", help="choose type of analysis", action="store")
+parser.add_argument("-con", "--control", help="input fastq file", nargs='+', default=[])
+parser.add_argument("-tre", "--treated", help="input fastq file", nargs='+', default=[] )
+parser.add_argument("-tool_dir", "--tool_directory", help="tool directory path", action="store")
+parser.add_argument("-gen", "--org_name", help="tool directory path", action="store")
+parser.add_argument("-program", "--pro", help="choose type of analysis", action="store")
+parser.add_argument("-f", "--flag", help="choose the database", action="store")
+parser.add_argument("-umis", "--umi", help="choose the database", action="store")
+parser.add_argument("-percentage", "--per", help="choose the database", action="store")
+parser.add_argument("-counts", "--count", help="choose the database", action="store")
+parser.add_argument("-name1", "--n1", help="choose the database", action="store")
+parser.add_argument("-name2", "--n2", help="choose the database", action="store")
+args = parser.parse_args()
+
+
+###############################################################################################################################################################################################
+
+if __name__ == '__main__':
+
+ starttime = time.time()
+
+ q1 = Queue()
+ q2 = Queue()
+ lock = Lock()
+ manager = Manager()
+
+ mature_mirnas=manager.list()
+ ps_mature=Process(target=download_matures,args=(mature_mirnas,args.org_name))
+ ps_mature.start()
+
+ args.control[0]=args.control[0][1:]
+ args.control[len(args.control)-1][:-1]
+ control = [(args.control[i:i+2]) for i in range(0, len(args.control), 2)]
+
+ args.treated[0]=args.treated[0][1:]
+ args.treated[len(args.treated)-1][:-1]
+ treated = [(args.treated[i:i+2]) for i in range(0, len(args.treated), 2)]
+
+
+##############  Detection of templated isoforms ################
+
+ radar = manager.list([0,0,0,0])
+ samples = manager.list()
+ data= manager.list()
+ names_con=manager.list()
+ samples_mirna_names=manager.list()
+ deseq=manager.list()
+ unmap_seq=manager.Value('i',0)
+ unmap_counts=manager.Value('i',0)
+ LH2E_names=manager.list()
+ ini_c_samples = manager.list()
+
+
+ radar1 = manager.list([0,0,0,0])
+ samples1 = manager.list()
+ data1 = manager.list()
+ names_tre = manager.list()
+ samples_mirna_names1=manager.list()
+ deseq1=manager.list()
+ unmap1_seq = manager.Value('i',0)
+ unmap1_counts = manager.Value('i',0)
+ LH8E_names=manager.list()
+ ini_t_samples = manager.list()
+ ps_mature.join()
+
+
+ mature_mirnas=list(mature_mirnas)
+
+
+ starttime1 = time.time()
+ ps_sam = [Process(target=sam,args=(mature_mirnas,path[1][:-1],path[0].split(",")[0],"c",lock,samples,data,names_con,unmap_seq,samples_mirna_names,deseq,LH2E_names,"0",ini_c_samples,unmap_counts)) for path in control]
+ ps_sam.extend([Process(target=sam,args=(mature_mirnas,path[1][:-1],path[0].split(",")[0],"t",lock,samples1,data1,names_tre,unmap1_seq,samples_mirna_names1,deseq1,LH8E_names,"0",ini_t_samples,unmap1_counts)) for path in treated])
+
+ [p.start() for p in ps_sam]
+ [p.join() for p in ps_sam]
+ print('SAM took {} seconds'.format(time.time() - starttime1))
+
+ ps_hist=[Process(target=hist_red,args=(ini_c_samples,'c'))]
+ ps_hist.extend([Process(target=hist_red,args=(ini_t_samples,'t'))])
+ [x.start() for x in ps_hist]
+
+ starttime200=time.time()
+
+ sc = list(samples)
+ st = list(samples1)
+
+ names_con=list(names_con)
+ names_tre=list(names_tre)
+ samples_mirna_names=list(samples_mirna_names)
+ samples_mirna_names.sort()
+ samples_mirna_names=list(samples_mirna_names for samples_mirna_names,_ in itertools.groupby(samples_mirna_names))
+
+ samples_mirna_names1=list(samples_mirna_names1)
+ samples_mirna_names1.sort()
+ samples_mirna_names1=list(samples_mirna_names1 for samples_mirna_names1,_ in itertools.groupby(samples_mirna_names1))
+
+ deseq=list(deseq)
+ deseq1=list(deseq1)
+
+ new_names_con=manager.list()
+ new_names_tre=manager.list()
+ new_deseq=manager.list()
+ new_deseq1=manager.list()
+ ps_deseq=[Process(target=deseqe2,args=(sampp,samples_mirna_names,lock,new_deseq,names_con[i],new_names_con)) for i,sampp in enumerate(deseq)]
+ ps_deseq.extend([Process(target=deseqe2,args=(sampp,samples_mirna_names1,lock,new_deseq1,names_tre[i],new_names_tre)) for i,sampp in enumerate(deseq1)])
+
+ [z.start() for z in ps_deseq]
+ [z.join() for z in ps_deseq]
+ new_deseq=list(new_deseq)
+ new_deseq1=list(new_deseq1)
+
+ LH2E=[[x[0],x[2]] for x in new_deseq[0]]
+ [LH2E[i].append(y[i][1]) for i,_ in enumerate(LH2E) for y in new_deseq]
+
+ LH8E=[[x[0],x[2]] for x in new_deseq1[0]]
+ [LH8E[i].append(y[i][1]) for i,_ in enumerate(LH8E) for y in new_deseq1]
+
+ print('Deseq took {} seconds'.format(time.time() - starttime200))
+
+ merg_nam_LH2E=manager.list()
+ merg_nam_LH8E=manager.list()
+
+ LH2E_copy=copy.deepcopy(list(LH2E))
+ LH8E_copy=copy.deepcopy(list(LH8E))
+
+ fil_sort_tre=manager.list()
+ fil_sort_con=manager.list()
+ raw_sort_tre=manager.list()
+ raw_sort_con=manager.list()
+
+ ps_main = Process(target=main_temp,args=(list(LH2E), samples_mirna_names, list(LH8E), samples_mirna_names1,1,list(names_con),list(names_tre),fil_sort_tre,fil_sort_con,raw_sort_tre,raw_sort_con))
+ ps_main.start()
+
+ if args.anal=="2":
+    all_iso = manager.list()
+    ps_non_iso = Process(target=non_template_ref,args=(sc,st,all_iso))
+    ps_non_iso.start()
+
+ ps_merge = [Process(target=merging_names,args=(LH2E_copy,merg_nam_LH2E))]
+ ps_merge.extend([Process(target=merging_names,args=(LH8E_copy,merg_nam_LH8E))])
+ [x.start() for x in ps_merge]
+ [x.join() for x in ps_merge]
+
+ merg_nam_LH2E=list(merg_nam_LH2E)
+ merg_nam_LH8E=list(merg_nam_LH8E)
+
+ starttime2 = time.time()
+ procs = [Process(target=DB_write,args=(x[0],x[1],x[2],x[3],1)) for x in data]
+ procs.extend([Process(target=DB_write,args=(x[0],x[1],x[2],x[3],1)) for x in data1])
+ procs.extend([Process(target=make_spider,args=(merg_nam_LH2E,merg_nam_LH8E))])
+ if args.anal == "1":
+    procs.extend([Process(target=pie_temp,args=(merg_nam_LH2E,unmap_seq.value,unmap_counts.value,merg_nam_LH8E,unmap1_seq.value,unmap1_counts.value))])
+
+ [p.start() for p in procs]
+
+
+ if args.anal=="1":
+    [x.join() for x in ps_hist]
+    [p.join() for p in procs]
+    ps_pdf = Process(target=pdf_before_DE,args=(args.anal))
+    ps_pdf.start()
+
+ print('Graphs took {} seconds'.format(time.time() - starttime2))
+
+ ps_main.join()
+
+ fil_sort_con=list(fil_sort_con)
+ fil_sort_tre=list(fil_sort_tre)
+ if fil_sort_con==[]:
+    fil_sort_con=raw_sort_con
+    fil_sort_tre=raw_sort_tre
+
+ raw_sort_con=list(raw_sort_con)
+ raw_sort_tre=list(raw_sort_tre)
+ names_con=list(new_names_con)
+ names_tre=list(new_names_tre)
+
+ ps_write = Process(target=write_main,args=(raw_sort_con, raw_sort_tre, fil_sort_con, fil_sort_tre, names_con,names_tre,1,args.per,args.n1,args.n2))
+ ps_write.start()
+
+ ps1_matrix = [Process(target=ssamples,args=(names_con,fil_sort_con,"Diff/temp_con/",0))]
+ ps1_matrix.extend([Process(target=ssamples,args=(names_tre,fil_sort_tre,"Diff/temp_tre/",0))])
+ [p.start() for p in ps1_matrix]
+
+ if args.anal=="1":
+    ps_pdf.join()
+ if args.anal=="2":
+    [p.join() for p in procs]
+    [x.join() for x in ps_hist]
+
+ ps_write.join()
+ [p.join() for p in ps1_matrix]
+
+
+############################## Detection of Both  #######################################
+
+ starttime10 = time.time()
+
+ if args.anal == "2":
+
+  n_data= manager.list()
+  n_names_con=manager.list()
+  n_samples_mirna_names=manager.list()
+  n_deseq=manager.list()
+  n_LH2E_names=manager.list()
+
+  n_data1 = manager.list()
+  n_names_tre = manager.list()
+  n_samples_mirna_names1=manager.list()
+  n_deseq1=manager.list()
+  n_LH8E_names=manager.list()
+
+
+  new_mat_mirnas = list(mature_mirnas)
+  ps_non_iso.join()
+
+  all_iso=list(all_iso)
+  new_mat_mirnas.extend(all_iso)
+
+  starttime11=time.time()
+
+  ps_sam = [Process(target=non_sam,args=(new_mat_mirnas,path[1][:-1],path[0].split(",")[0],"c",lock,n_data,n_names_con,n_deseq,n_samples_mirna_names,n_LH2E_names)) for path in control]
+  ps_sam.extend([Process(target=non_sam,args=(new_mat_mirnas,path[1][:-1],path[0].split(",")[0],"t",lock,n_data1,n_names_tre,n_deseq1,n_samples_mirna_names1,n_LH8E_names)) for path in treated])
+
+  [p.start() for p in ps_sam]
+  [p.join() for p in ps_sam]
+
+  print('Non-sam took {} seconds'.format(time.time() - starttime11))
+
+  starttime12=time.time()
+
+  n_names_con=list(n_names_con)
+  n_names_tre=list(n_names_tre)
+  n_samples_mirna_names=list(n_samples_mirna_names)
+  n_samples_mirna_names.sort()
+  n_samples_mirna_names=list(n_samples_mirna_names for n_samples_mirna_names,_ in itertools.groupby(n_samples_mirna_names))
+
+  n_samples_mirna_names1=list(n_samples_mirna_names1)
+  n_samples_mirna_names1.sort()
+  n_samples_mirna_names1=list(n_samples_mirna_names1 for n_samples_mirna_names1,_ in itertools.groupby(n_samples_mirna_names1))
+
+  n_deseq=list(n_deseq)
+  n_deseq1=list(n_deseq1)
+
+  new_n_names_con=manager.list()
+  new_n_names_tre=manager.list()
+  n_new_deseq=manager.list()
+  n_new_deseq1=manager.list()
+  ps_deseq=[Process(target=deseqe2,args=(sampp,n_samples_mirna_names,lock,n_new_deseq,n_names_con[i],new_n_names_con)) for i,sampp in enumerate(n_deseq)]
+  ps_deseq.extend([Process(target=deseqe2,args=(sampp,n_samples_mirna_names1,lock,n_new_deseq1,n_names_tre[i],new_n_names_tre)) for i,sampp in enumerate(n_deseq1)])
+
+  [x.start() for x in ps_deseq]
+  [x.join() for x in ps_deseq]
+  n_new_deseq=list(n_new_deseq)
+  n_new_deseq1=list(n_new_deseq1)
+
+  n_LH2E=[[x[0],x[2]] for x in n_new_deseq[0]]
+  [n_LH2E[i].append(y[i][1]) for i,_ in enumerate(n_LH2E) for y in n_new_deseq]
+
+  n_LH8E=[[x[0],x[2]] for x in n_new_deseq1[0]]
+  [n_LH8E[i].append(y[i][1]) for i,_ in enumerate(n_LH8E) for y in n_new_deseq1]
+
+  print('Non-deseq took {} seconds'.format(time.time() - starttime12))
+
+  merg_nam_n_LH2E=manager.list()
+  merg_nam_n_LH8E=manager.list()
+
+  n_LH2E_copy=copy.deepcopy(list(n_LH2E))
+  n_LH8E_copy=copy.deepcopy(list(n_LH8E))
+
+  n_sort_tre=manager.list()
+  n_sort_con=manager.list()
+
+  n_fil_sort_con=manager.list()
+  n_fil_sort_tre=manager.list()
+  n_raw_sort_con=manager.list()
+  n_raw_sort_tre=manager.list()
+
+  ps_main = Process(target=main_temp,args=(list(n_LH2E), n_samples_mirna_names, list(n_LH8E), n_samples_mirna_names1,1,list(n_names_con),list(n_names_tre),n_fil_sort_tre,n_fil_sort_con,n_raw_sort_tre,n_raw_sort_con))
+  ps_main.start()
+
+  ps_merge = [Process(target=merging_names,args=(n_LH2E_copy,merg_nam_n_LH2E))]
+  ps_merge.extend([Process(target=merging_names,args=(n_LH8E_copy,merg_nam_n_LH8E))])
+  [p.start() for p in ps_merge]
+  [p.join() for p in ps_merge]
+
+  merg_nam_n_LH2E=list(merg_nam_n_LH2E)
+  merg_nam_n_LH8E=list(merg_nam_n_LH8E)
+
+  procs = [Process(target=DB_write,args=(x[0],x[1],x[2],x[3],2)) for x in n_data]
+  procs.extend([Process(target=DB_write,args=(x[0],x[1],x[2],x[3],2)) for x in n_data1])
+  procs.extend([Process(target=logo_seq_red,args=(merg_nam_n_LH2E,'c'))])
+  procs.extend([Process(target=logo_seq_red,args=(merg_nam_n_LH8E,'t'))])
+  procs.extend([Process(target=pie_non_temp,args=(merg_nam_LH2E,merg_nam_n_LH2E,merg_nam_LH8E,merg_nam_n_LH8E,unmap_seq.value,unmap1_seq.value,unmap_counts.value,unmap1_counts.value))])
+
+  starttime13=time.time()
+  [p.start() for p in procs]
+  [p.join() for p in procs]
+
+  print('Graphs took {} seconds'.format(time.time() - starttime13))
+
+  procs1 = Process(target=pdf_before_DE,args=(args.anal))
+  procs1.start()
+
+  starttime14=time.time()
+  ps_main.join()
+
+  n_fil_sort_con=list(n_fil_sort_con)
+  n_fil_sort_tre=list(n_fil_sort_tre)
+  if n_fil_sort_con==[]:
+     n_fil_sort_con=n_raw_sort_con
+     n_fil_sort_tre=n_raw_sort_tre
+
+  n_raw_sort_con=list(n_raw_sort_con)
+  n_raw_sort_tre=list(n_raw_sort_tre)
+  n_names_con=list(new_n_names_con)
+  n_names_tre=list(new_n_names_tre)
+
+  ps_write = Process(target=write_main,args=(n_raw_sort_con, n_raw_sort_tre,n_fil_sort_con, n_fil_sort_tre, n_names_con, n_names_tre,2,args.per,args.n1,args.n2))
+  ps_write.start()
+
+  ps1_matrix = [Process(target=ssamples1,args=(n_names_con,n_fil_sort_con,names_con,fil_sort_con,"Diff/n_temp_con/",0))]
+  ps1_matrix.extend([Process(target=ssamples1,args=(n_names_tre,n_fil_sort_tre,names_tre,fil_sort_tre,"Diff/n_temp_tre/",0))])
+  [p.start() for p in ps1_matrix]
+
+  ps_write.join()
+  [p.join() for p in ps1_matrix]
+  procs1.join()
+ print('That took {} seconds'.format(time.time() - starttime10))
+ print('That took {} seconds'.format(time.time() - starttime))
+
+
+
+
+
+
+
+