diff libs/run_auto_All_for_assemblies.py @ 10:53efef402c51 draft

planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty

--- a/libs/run_auto_All_for_assemblies.py	Tue Nov 28 21:16:36 2017 -0500
+++ b/libs/run_auto_All_for_assemblies.py	Wed Nov 29 08:34:19 2017 -0500
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python2.7
 
 
 
@@ -51,11 +51,11 @@
     real_file=file2
   except:
     real_file=file1
-  #print("###The genome name:",file1
+  #print "###The genome name:",file1
   dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))###01/27/2015
   os.system('touch result.txt')
   database_path="database"###01/27/2015
-  os.system('python '+dirpath+'/Otype_determine_analysis.py '+database_path+'/Typhimurium_LT2_gnd_galF.fasta '+real_file+' '+database_path+'/new_Oserotype.fasta >temp_result_'+str(q)+'O.txt')
+  os.system('python2.7 '+dirpath+'/Otype_determine_analysis.py '+database_path+'/Typhimurium_LT2_gnd_galF.fasta '+real_file+' '+database_path+'/new_Oserotype.fasta >temp_result_'+str(q)+'O.txt')
   os.system('cat temp_result_'+str(q)+'O.txt>>data_log.txt')
   handle=open('temp_result_'+str(q)+'O.txt',"r")
   handle=handle.readlines()
@@ -81,8 +81,8 @@
     elif O1_3_19=="+":
       Otype="1,3,19"
     else:
-      print("No_O3,10_O1,3,19_spe_sequences")
-  os.system('python '+dirpath+'/H_combination_output_analysis.py '+real_file+' '+database_path+'/H_new_fliC_protein_database.fasta '+database_path+'/H_new_fljB_protein_database.fasta >temp_result_'+str(q)+'H.txt')
+      print "No_O3,10_O1,3,19_spe_sequences"
+  os.system('python2.7 '+dirpath+'/H_combination_output_analysis.py '+real_file+' '+database_path+'/H_new_fliC_protein_database.fasta '+database_path+'/H_new_fljB_protein_database.fasta >temp_result_'+str(q)+'H.txt')
   os.system('cat temp_result_'+str(q)+'H.txt>>data_log.txt')
   handle2=open('temp_result_'+str(q)+'H.txt',"r")
   handle2=handle2.readlines()
@@ -103,7 +103,7 @@
       fljB="-"
       #print line,
   if Otype=="9" and fliC=="g,m" and fljB=="-":
-    os.system('python '+dirpath+'/special_gene_test_assemblies.py '+database_path+'/specific_genes.fasta '+real_file+' sdf >temp_result_'+str(q)+'sdf.txt')
+    os.system('python2.7 '+dirpath+'/special_gene_test_assemblies.py '+database_path+'/specific_genes.fasta '+real_file+' sdf >temp_result_'+str(q)+'sdf.txt')
     os.system('cat temp_result_'+str(q)+'sdf.txt>>data_log.txt')
     handle3=open('temp_result_'+str(q)+'sdf.txt',"r")
     sdf=""
@@ -166,18 +166,18 @@
   if len(seronames)>1:
     star="*"
     star_line="The predicted serotypes share the same general formula:\t"+Otype+":"+fliC+":"+fljB+"\n"##
-  #print("$$$The most possible formula is: (by the order O:H1:H2) ",Otype,":",fliC,":",fljB
-  #print("$$$The possible serotyes are:",seronames
+  #print "$$$The most possible formula is: (by the order O:H1:H2) ",Otype,":",fliC,":",fljB
+  #print "$$$The possible serotyes are:",seronames
   m=0
   for y in seronames:
     if y in file1:
-      #print("$$$ Is the judgement true? Answer:Yes!"       #here we use file1, because we want ":", while file2 turned it to "__"
+      #print "$$$ Is the judgement true? Answer:Yes!"       #here we use file1, because we want ":", while file2 turned it to "__"
       answer="Yes"
       m=1
   if m==0:
-    #print("$$$ Is the judgement true? Answer: Need to check the records and file names"
+    #print "$$$ Is the judgement true? Answer: Need to check the records and file names"
     answer="Not sure"
-  print("\n","\n")
+  print "\n","\n"
   predict_form=Otype+":"+fliC+":"+fljB
   predict_sero=(" or ").join(seronames)
   if predict_form=="9:g,m:-":#
@@ -250,12 +250,12 @@
       txt_names.append(file_names[j+i].replace(' ','_').replace(":","__").replace("[","").replace("]","")+".txt")
     print txt_names
     for j in xrange(len(txt_names)):
-      print(i,"and",j)
-      print(i+j+1)
+      print i,"and",j
+      print i+j+1
       file=open(txt_names[j],"r")
       handle=list(file)
       b=handle[0].split("\t")
-      print(b)
+      print b
       sheet.write(i+j+1,0,b[0])
       sheet.write(i+j+1,1,b[1])
       sheet.write(i+j+1,2,b[2])
@@ -265,7 +265,7 @@
       sheet.write(i+j+1,6,b[6])
       sheet.write(i+j+1,7,b[7])
 
-  print("End time,",time.time())
+  print "End time,",time.time()
   file3.save("Seqsero_result2.xls")
   '''