--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/viz.py	Wed Oct 13 11:19:17 2021 +0000
@@ -0,0 +1,96 @@
+from viz_graphs import *
+from viz_functions import *
+import argparse
+import time
+from multiprocessing import Process, Lock, Manager
+
+##################################################################################################################################################################################################################################################################
+starttime = time.time()
+
+parser = argparse.ArgumentParser()
+parser.add_argument("-in", "--input", help="choose type of analysis", action="store")
+parser.add_argument("-p_value", "--pval", help="choose type of analysis", action="store")
+parser.add_argument("-fc", "--log2fc", help="choose type of analysis", action="store")
+parser.add_argument("-top", "--top_mirnas", help="choose type of analysis", action="store")
+parser.add_argument("-tool_dir", "--tool_directory", help="tool directory path", action="store")
+parser.add_argument("-statistic", "--stat", help="tool directory path", action="store")
+parser.add_argument("-diff_tool", "--tool", help="tool directory path", action="store")
+
+args = parser.parse_args()
+
+l=Lock()
+number = int(args.top_mirnas)
+log2fc = float(args.log2fc)
+pval = float(args.pval)
+iso_star_flag=0
+non_star_flag=0
+
+if args.tool=="2":
+
+   raw_EdgeR = read(args.input,0)
+   EdgeR = [x.rstrip("\n").split("\t") for x in raw_EdgeR]
+   del EdgeR[0]
+   for x in EdgeR:
+       if "/" in x[0]:
+           x[0]=x[0].split("/")[0]+"★"
+
+   if args.stat=="1":
+      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"]
+      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"]
+      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"]
+   else:
+      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"]
+      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"]
+      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"]
+
+if args.tool=="1":
+
+   raw_Deseq = read(args.input,0)
+   Deseq = [x.rstrip("\n").split("\t") for x in raw_Deseq]
+   for x in Deseq:
+       if "/" in x[0]:
+           x[0]=x[0].split("/")[0]+"★"
+
+   if args.stat=="1":
+      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"]
+      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"]
+      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"]
+   elif args.stat=="2":
+      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"]
+      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"]
+      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"]
+   else:
+      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"]
+      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"]
+      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"]
+
+
+diff_matures,diff_isoforms,diff_non_templated,names,non_temp,mat_iso = preproccess(non_templated,matures,isoforms,log2fc,pval,args.stat)
+for x in mat_iso[:number]:
+    if "★" in x[0]:
+        iso_star_flag=1
+        break
+for x in non_temp[:number]:
+    if "★" in x[0]:
+        non_star_flag=1
+        break
+
+
+if non_templated!=[]:
+   analysis="2"
+   p=[Process(target=top_diff,args=(non_temp,number,"nt",l))]
+   p.extend([Process(target=top_diff,args=(mat_iso,number,"t",l))])
+   p.extend([Process(target=top_scatter_non,args=(diff_matures,diff_isoforms,diff_non_templated,names,number))])
+
+else:
+   analysis="1"
+   p=[Process(target=top_diff,args=(mat_iso,number,"t",l))]
+   p.extend([Process(target=top_scatter_tem,args=(diff_matures,diff_isoforms,names,number))])
+
+[x.start() for x in p]
+[x.join() for x in p]
+
+pdf_after_DE(analysis,args.top_mirnas,args.tool_directory,iso_star_flag,non_star_flag)
+
+print('That took {} seconds'.format(time.time() - starttime))
+