# HG changeset patch
# User charles_s_test
# Date 1511962459 18000
# Node ID 53efef402c516a49f10d24e882b5f832e36ad6c2
# Parent  acc5cd06a36a46a925617aa93c44f6ce0b4b90e4
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty

diff -r acc5cd06a36a -r 53efef402c51 SeqSero.py
--- a/SeqSero.py	Tue Nov 28 21:16:36 2017 -0500
+++ b/SeqSero.py	Wed Nov 29 08:34:19 2017 -0500
@@ -26,11 +26,11 @@
     mapping_mode=args.b
     dataset=args.i
     if mode_choice=="1":
-      print(dataset[0])
+      print dataset[0]
       os.system("cp "+dataset[0]+" "+make_dir)
       os.chdir(make_dir)
       os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_web_multi_revise.py "+dataset[0].split("/")[-1]+" "+mapping_mode+" 1")
-      print("\n\n\nResult:\n")
+      print "\n\n\nResult:\n"
       os.system("cat Seqsero_result.txt")
       os.system("rm "+dataset[0].split("/")[-1])
     elif mode_choice=="2":
@@ -39,21 +39,21 @@
       fnameA=dataset[0].split("/")[-1]
       fnameB=dataset[1].split("/")[-1]
       os.chdir(make_dir)
-      print("check fastq id and make them in accordance with each other...please wait...")
+      print "check fastq id and make them in accordance with each other...please wait..."
       os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_web_multi_revise.py "+fnameA+" "+mapping_mode+" "+fnameB+" 2")
-      print("\n\n\nResult:\n")
+      print "\n\n\nResult:\n"
       os.system("cat Seqsero_result.txt")
     elif mode_choice=="3":
       os.system("cp "+dataset[0]+" "+make_dir)
       os.chdir(make_dir)
       os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_web_multi_revise.py "+dataset[0].split("/")[-1]+" "+mapping_mode+" 3")
-      print("\n\n\nResult:\n")
+      print "\n\n\nResult:\n"
       os.system("cat Seqsero_result.txt")
     elif mode_choice=="4":
       os.system("cp "+dataset[0]+" "+make_dir)
       os.chdir(make_dir)
       os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_assemblies.py "+dataset[0].split("/")[-1])
-      print("\n\n\nResult:\n")
+      print "\n\n\nResult:\n"
       os.system("cat Seqsero_result.txt")
 
 if __name__ == '__main__':
diff -r acc5cd06a36a -r 53efef402c51 Seqsero_result.html
--- a/Seqsero_result.html	Tue Nov 28 21:16:36 2017 -0500
+++ b/Seqsero_result.html	Wed Nov 29 08:34:19 2017 -0500
@@ -15,6 +15,21 @@
 <td>Predicted antigenic profile</td>
 <td>Predicted serotype(s)</td>
 </tr>
+<tr>
+<td>dataset_170_SRR6325381.fastq dataset_171_SRR6325381.fastq</td>
+<td>O-3,10</td>
+<td>e,h</td>
+<td>1,6</td>
+<td>3,10:e,h:1,6</td>
+<td>Anatum</td>
+</tr>
 </table>
+<tr>
+<p>
+<td>dataset_170_SRR6325381.fastq dataset_171_SRR6325381.fastq<br></td>
+<td>The serotype(s) is/are the only serotype(s) with the indicated antigenic profile currently recognized in the Kauffmann White Scheme.  New serotypes can emerge and the possibility exists that this antigenic profile may emerge in a different subspecies.  Identification of strains to the subspecies level should accompany serotype determination; the same antigenic profile in different subspecies is considered different serotypes.</td>
+<td>check fastq id and make them in accordance with each other...please wait...</td>
+</p>
+</tr>
 </body>
 </html>
diff -r acc5cd06a36a -r 53efef402c51 Seqsero_result.txt
--- a/Seqsero_result.txt	Tue Nov 28 21:16:36 2017 -0500
+++ b/Seqsero_result.txt	Wed Nov 29 08:34:19 2017 -0500
@@ -1,1 +1,6 @@
 Input_Files	O_antigen_prediction	H1_antigen_prediction(fliC)	H2_antigen_prediction(fljB)	Predicted_antigenic_profile	Predicted_serotype(s)
+dataset_170_SRR6325381.fastq dataset_171_SRR6325381.fastq	O-3,10	e,h	1,6	3,10:e,h:1,6	Anatum
+
+dataset_170_SRR6325381.fastq dataset_171_SRR6325381.fastq
+The serotype(s) is/are the only serotype(s) with the indicated antigenic profile currently recognized in the Kauffmann White Scheme.  New serotypes can emerge and the possibility exists that this antigenic profile may emerge in a different subspecies.  Identification of strains to the subspecies level should accompany serotype determination; the same antigenic profile in different subspecies is considered different serotypes.
+check fastq id and make them in accordance with each other...please wait...
diff -r acc5cd06a36a -r 53efef402c51 libs/BWA_analysis_H_update_new_family_dependent.py
--- a/libs/BWA_analysis_H_update_new_family_dependent.py	Tue Nov 28 21:16:36 2017 -0500
+++ b/libs/BWA_analysis_H_update_new_family_dependent.py	Wed Nov 29 08:34:19 2017 -0500
@@ -104,23 +104,23 @@
   for x in c:
     if x[:4]=="fljB":
       fljB[x]=c[x]
-  final_fliC=sorted(fliC.items(), key=lambda d:d[1], reverse = True) #order from frequency high to low, but tuple while not list
-  final_fljB=sorted(fljB.items(), key=lambda d:d[1], reverse = True) #order from frequency high to low, but tuple while not list
-  print("Final_filC_list:")
-  print(final_fliC)
+  final_fliC=sorted(fliC.iteritems(), key=lambda d:d[1], reverse = True) #order from frequency high to low, but tuple while not list
+  final_fljB=sorted(fljB.iteritems(), key=lambda d:d[1], reverse = True) #order from frequency high to low, but tuple while not list
+  print "Final_filC_list:"
+  print final_fliC
   num_1=0#new inserted
   num_2=0#new inserted
   if len(final_fliC)>0: #new inserted
     for x in final_fliC:#new inserted
       num_1=num_1+x[1]#new inserted
-  print("Final_fliC_number_together: ",num_1)#new inserted
-  print("Final_fljB_list:")
-  print(final_fljB)
+  print "Final_fliC_number_together: ",num_1#new inserted
+  print "Final_fljB_list:"
+  print final_fljB
   if len(final_fljB)>0: #new inserted
     for x in final_fljB: #new inserted
       num_2=num_2+x[1] #new inserted
-  print("Final_fljB_number_together: ",num_2)#new inserted
-  print("$$Genome:",sra_name)
+  print "Final_fljB_number_together: ",num_2#new inserted
+  print "$$Genome:",sra_name
   try:
     fliC_option=final_fliC[0][0].split("_")[1]
   except:
@@ -132,16 +132,16 @@
    
   if z==0:
     if len(final_fliC)==0 or num_1<=10:
-      print("$$$No fliC, due to no hit")
+      print "$$$No fliC, due to no hit"
     else:
       if final_fliC[0][1]<=1 and z==1:
-        print("$$$No fliC, due to the hit reads number is small.")
+        print "$$$No fliC, due to the hit reads number is small."
       else:
         try:
           family=final_fliC[0][0].split("_")[-1]
           Sero_list_C.append(family)
           description.append(final_fliC[0][0])
-          print("$$Most possilble fliC family: ",Sero_list_C[0]," Number: ",final_fliC[0][1])
+          print "$$Most possilble fliC family: ",Sero_list_C[0]," Number: ",final_fliC[0][1]
           i=0
           for x in final_fliC:
             if x[0].split("_")[-1] not in Sero_list_C:
@@ -153,7 +153,7 @@
           if locals().has_key('sec_choice'):
             Sero_list_C.append(sec_choice)
             description.append(des)
-            print("$$Sec possilble fliC family: ",sec_choice," Number: ",number)
+            print "$$Sec possilble fliC family: ",sec_choice," Number: ",number
             j=0
             for x in final_fliC:
               if x[0].split("_")[-1] not in Sero_list_C:
@@ -165,25 +165,25 @@
             if locals().has_key('third_choice'):
               Sero_list_C.append(third_choice)
               description.append(des)
-              print("$$Third possilble fliC family: ",third_choice," Number: ",number)
+              print "$$Third possilble fliC family: ",third_choice," Number: ",number 
         except:
-          print("$$$No fliC, or failure of mapping")
+          print "$$$No fliC, or failure of mapping"
     try:
       ratio=float(num_2)/float(num_1)
     except:
       ratio=0
 
     if len(final_fljB)==0 or num_2<=5 or ratio<0.15:
-      print("$$$No fljB, due to no hit")
+      print "$$$No fljB, due to no hit"
     else:
       if final_fljB[0][1]<=1 and z==1:
-        print("$$$No fljB, due to the hit reads number is small.")
+        print "$$$No fljB, due to the hit reads number is small."
       else:
         try:
           family=final_fljB[0][0].split("_")[-1]
           Sero_list_B.append(family)
           description.append(final_fljB[0][0])
-          print("$$Most possilble fljB family: ",Sero_list_B[0]," Number: ",final_fljB[0][1])
+          print "$$Most possilble fljB family: ",Sero_list_B[0]," Number: ",final_fljB[0][1]
           i=0
           for x in final_fljB:
             if x[0].split("_")[-1] not in Sero_list_B:
@@ -195,7 +195,7 @@
           if locals().has_key('B_sec_choice'):
             Sero_list_B.append(B_sec_choice)
             description.append(des)
-            print("$$Sec possilble fljB: ",B_sec_choice," Number: ",number)  
+            print "$$Sec possilble fljB: ",B_sec_choice," Number: ",number   
             j=0
             for x in final_fljB:
               if x[0].split("_")[-1] not in Sero_list_B:
@@ -207,9 +207,9 @@
             if locals().has_key('B_third_choice'):
               Sero_list_B.append(B_third_choice)
               description.append(des)
-              print("$$Third possilble fljB: ",B_third_choice," Number: ",number)
+              print "$$Third possilble fljB: ",B_third_choice," Number: ",number 
         except:
-          print("$$$No fljB, or failure of mapping")
+          print "$$$No fljB, or failure of mapping"
     if len(description)==0:    #used for the case which fljB and fliC both has no hit, it will directly cease the function
       return
     handle=SeqIO.parse("database/"+database,"fasta")########1/27/2015
@@ -250,10 +250,10 @@
   Sero_list_B=[]
   if listtype=="fliC":
     if len(fliC_fljB_list)==0:
-      print("$$No fliC, due to no hit") #because the only possible situation for len(final_fliC)==0 is above (z=0) len(final_fliC)==0, so there is no need to use "$$$" here
+      print "$$No fliC, due to no hit" #because the only possible situation for len(final_fliC)==0 is above (z=0) len(final_fliC)==0, so there is no need to use "$$$" here
     else:
       if fliC_fljB_list[0][1]<=1:
-        print("$$No fliC, due to the hit reads number is small.") #similiar with above, no "$$$"
+        print "$$No fliC, due to the hit reads number is small." #similiar with above, no "$$$"
       else:
         if fliC_fljB_list[0][0].split("_")[-1]=="g,m":
           type="fliC"
@@ -293,7 +293,7 @@
         else:
           try: 
             Sero_list_C.append(fliC_fljB_list[0][0].split("_")[1])
-            print("$$$Most possilble fliC: ",Sero_list_C[0]," Number: ",fliC_fljB_list[0][1])
+            print "$$$Most possilble fliC: ",Sero_list_C[0]," Number: ",fliC_fljB_list[0][1]
             i=0
             for x in fliC_fljB_list:
               if x[0].split("_")[1] not in Sero_list_C:
@@ -303,7 +303,7 @@
                   number=x[1]
             if locals().has_key('sec_choice'):
               Sero_list_C.append(sec_choice)
-              print("$$$Sec possilble fliC: ",sec_choice," Number: ",number)
+              print "$$$Sec possilble fliC: ",sec_choice," Number: ",number
               j=0
               for x in fliC_fljB_list:
                 if x[0].split("_")[1] not in Sero_list_C:
@@ -313,16 +313,16 @@
                     number=x[1]
               if locals().has_key('third_choice'):
                 Sero_list_C.append(third_choice)
-                print("$$$Third possilble fliC: ",third_choice," Number: ",number)
+                print "$$$Third possilble fliC: ",third_choice," Number: ",number 
           except:
-            print("$$$No fliC, or failure of mapping (second run)")
+            print "$$$No fliC, or failure of mapping (second run)"
 
   if listtype=="fljB":
     if len(fliC_fljB_list)==0:
-      print("$$No fljB, due to no hit") #similiar with above, no "$$$"
+      print "$$No fljB, due to no hit" #similiar with above, no "$$$"
     else:
       if fliC_fljB_list[0][1]<=1:
-        print("$$No fljB, due to the hit reads number is small.") #similiar with above, no "$$$"
+        print "$$No fljB, due to the hit reads number is small." #similiar with above, no "$$$"
       else:
         if fliC_fljB_list[0][0].split("_")[-1]=="1":
           type="fljB"
@@ -347,7 +347,7 @@
         else:
           try: 
             Sero_list_B.append(fliC_fljB_list[0][0].split("_")[1])
-            print("$$$Most possilble fljB: ",Sero_list_B[0]," Number: ",fliC_fljB_list[0][1])
+            print "$$$Most possilble fljB: ",Sero_list_B[0]," Number: ",fliC_fljB_list[0][1]
             i=0
             for x in fliC_fljB_list:
               if x[0].split("_")[1] not in Sero_list_B:
@@ -357,7 +357,7 @@
                   number=x[1]
             if locals().has_key('B_sec_choice'):
               Sero_list_B.append(B_sec_choice)
-              print("$$$Sec possilble fljB: ",B_sec_choice," Number: ",number)   
+              print "$$$Sec possilble fljB: ",B_sec_choice," Number: ",number   
               j=0
               for x in fliC_fljB_list:
                 if x[0].split("_")[1] not in Sero_list_B:
@@ -367,9 +367,9 @@
                     number=x[1]
               if locals().has_key('B_third_choice'):
                 Sero_list_B.append(B_third_choice)
-                print("$$$Third possilble fljB: ",B_third_choice," Number: ",number)
+                print "$$$Third possilble fljB: ",B_third_choice," Number: ",number 
           except:
-            print("$$$No fljB, or failure of mapping (second run)")
+            print "$$$No fljB, or failure of mapping (second run)"
 
 
 def assembly(type,sra_name,for_fq,rev_fq,for_sai,rev_sai,sam,bam,database,database2,list_length,mapping_mode):
@@ -421,18 +421,18 @@
             score+=handle[i].alignments[j].hsps[z].bits
       List_score.append(score)
   temp=dict(zip(List,List_score))
-  Final_list=sorted(temp.items(), key=lambda d:d[1], reverse = True)
+  Final_list=sorted(temp.iteritems(), key=lambda d:d[1], reverse = True)
   family=database2.split("_")[2]
   try:
-    Final_list[0][0].split("_")[1] # or it will always print("$$$Genome...."(next line)
-    print("$$$Genome:",sra_name)
-    print("$$$Most possilble "+type+": ",Final_list[0][0].split("_")[1]," Score(due_to_special_test, number changed to score): ",Final_list[0][1])
-    print(Final_list)
+    Final_list[0][0].split("_")[1] # or it will always print "$$$Genome...."(next line)
+    print "$$$Genome:",sra_name
+    print "$$$Most possilble "+type+": ",Final_list[0][0].split("_")[1]," Score(due_to_special_test, number changed to score): ",Final_list[0][1]
+    print Final_list
   except:
     if type=="fliC":
-      print("$$$There may be no hit for "+type+"_"+family+" family due to the reads not covering core seqeunce, but just based on reads hit number, the most possible one is: ",fliC_option)
+      print "$$$There may be no hit for "+type+"_"+family+" family due to the reads not covering core seqeunce, but just based on reads hit number, the most possible one is: ",fliC_option
     if type=="fljB":
-      print("$$$There may be no hit for "+type+"_"+family+" family due to the reads not covering core seqeunce, but just based on reads hit number, the most possible one is: ",fljB_option)
+      print "$$$There may be no hit for "+type+"_"+family+" family due to the reads not covering core seqeunce, but just based on reads hit number, the most possible one is: ",fljB_option
   os.system("rm "+database2+"_vs_"+sam+".xml")###01/28/2015
   os.system("rm "+database+sam+"_seq.txt")###01/28/2015
   os.system("rm "+database+sam+"_title.txt")###01/28/2015
diff -r acc5cd06a36a -r 53efef402c51 libs/BWA_analysis_O_new_dependent.py
--- a/libs/BWA_analysis_O_new_dependent.py	Tue Nov 28 21:16:36 2017 -0500
+++ b/libs/BWA_analysis_O_new_dependent.py	Wed Nov 29 08:34:19 2017 -0500
@@ -64,7 +64,7 @@
     for_fq=for_core_id+".fastq"
     rev_fq=re_core_id+".fastq"
     dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))#######03152016
-    print("check fastq id and make them in accordance with each other...please wait...")
+    print "check fastq id and make them in accordance with each other...please wait..."
     os.system("python "+dirpath+"/compare_and_change_two_fastq_id.py "+for_fq+" "+rev_fq)#######03152016
     for_sai=for_core_id+".sai"
     rev_sai=re_core_id+".sai"
@@ -117,8 +117,8 @@
   c=dict(zip(a,b))
   final_O=sorted(c.iteritems(), key=lambda d:d[1], reverse = True) #order from frequency high to low, but tuple while not list
   Sero_list_O=[]
-  print("Final_Otype_list:")
-  print(final_O)
+  print "Final_Otype_list:"
+  print final_O
   num_1=0#new inserted
   O9_wbav=0
   O310_wzx=0
@@ -140,12 +140,12 @@
   O_choice=""
 
 
-  print("$$$Genome:",sra_name)
+  print "$$$Genome:",sra_name
   if len(final_O)==0:
-    print("$$$No Otype, due to no hit")
+    print "$$$No Otype, due to no hit"
   else:
     if final_O[0][1]<8:
-      print("$$$No Otype, due to the hit reads number is small.")
+      print "$$$No Otype, due to the hit reads number is small."
     else:
       for x in final_O:
         if x[1]>5:
@@ -154,17 +154,17 @@
       for x in final_O:#
         if "sdf" in x[0] and x[1]>3:#
           qq=0#
-          print("$$$",x[0],"got a hit, reads:",x[1])#
+          print "$$$",x[0],"got a hit, reads:",x[1]#
       if qq!=0:#
-        print("$$$No sdf exists")#
+        print "$$$No sdf exists"#
 
       if "O-9,46_wbaV" in O_list and float(O9_wbaV)/float(num_1) > 0.1:
         if "O-9,46_wzy" in O_list and float(O946_wzy)/float(num_1) > 0.1:
           O_choice="O-9,46"
-          print("$$$Most possilble Otype:  O-9,46")
+          print "$$$Most possilble Otype:  O-9,46"
         elif "O-9,46,27_partial_wzy" in O_list and float(O94627)/float(num_1) > 0.1:
           O_choice="O-9,46,27"
-          print("$$$Most possilble Otype:  O-9,46,27")
+          print "$$$Most possilble Otype:  O-9,46,27"
         else:
           O_choice="O-9"
           if file_mode=="3":
@@ -176,18 +176,18 @@
       elif ("O-3,10_wzx" in O_list) and ("O-9,46_wzy" in O_list) and float(O310_wzx)/float(num_1) > 0.1 and float(O946_wzy)/float(num_1) > 0.1:
         if "O-3,10_not_in_1,3,19" in O_list and float(O310_no_1319)/float(num_1) > 0.1:
           O_choice="O-3,10"
-          print("$$$Most possilble Otype:  O-3,10")
+          print "$$$Most possilble Otype:  O-3,10"
         else:
           O_choice="O-1,3,19"
-          print("$$$Most possilble Otype:  O-1,3,19")
+          print "$$$Most possilble Otype:  O-1,3,19"
       else:
         try: 
           O_choice=final_O[0][0].split("_")[0]
           if O_choice=="O-1,3,19":
             O_choice=final_O[1][0].split("_")[0]
-          print("$$$Most possilble Otype: ",O_choice)
+          print "$$$Most possilble Otype: ",O_choice
         except:
-          print("$$$No suitable Otype, or failure of mapping (please check the quality of raw reads)")
+          print "$$$No suitable Otype, or failure of mapping (please check the quality of raw reads)"
 
 
 def assembly(sra_name,potential_choice,for_fq,rev_fq,for_sai,rev_sai,sam,bam,mapping_mode):
@@ -246,15 +246,15 @@
         O2_bigger+=1
     except:
       continue
-  print("$$$Genome:",sra_name)
+  print "$$$Genome:",sra_name
   if O9_bigger>O2_bigger:
-    print("$$$Most possible Otype is O-9")
+    print "$$$Most possible Otype is O-9"
   elif O9_bigger<O2_bigger:
-    print("$$$Most possible Otype is O-2")
+    print "$$$Most possible Otype is O-2"
   else:
-    print("$$$No suitable one, because can't distinct it's O-9 or O-2, but ",potential_choice," has a more possibility.")
-  print("O-9 number is:",O9_bigger)
-  print("O-2 number is:",O2_bigger)
+    print "$$$No suitable one, because can't distinct it's O-9 or O-2, but ",potential_choice," has a more possibility."
+  print "O-9 number is:",O9_bigger
+  print "O-2 number is:",O2_bigger
 
   os.system("rm "+sam+"_title.txt")###01/28/2015
   os.system("rm "+sam+"_seq.txt")###01/28/2015
diff -r acc5cd06a36a -r 53efef402c51 libs/H_combination_output_analysis.py
--- a/libs/H_combination_output_analysis.py	Tue Nov 28 21:16:36 2017 -0500
+++ b/libs/H_combination_output_analysis.py	Wed Nov 29 08:34:19 2017 -0500
@@ -225,21 +225,21 @@
           combination_score.append(score)
   combinationlist=dict(zip(combination,combination_score))  #we can do the filteration here
   final_dict=sorted(combinationlist.iteritems(), key=lambda d:d[1], reverse = True)
-  print("$$_H:Order:",final_dict)
+  print "$$_H:Order:",final_dict
 elif score>100 and fljB_score<100:
-  print("$$_H:No fljB, only fliC, and its order:",First_Choice,Sec_Choice,Third_Choice)
+  print "$$_H:No fljB, only fliC, and its order:",First_Choice,Sec_Choice,Third_Choice
 elif score<100 and fljB_score>100:
-  print("$$_H:No fliC, only fljB, and its order:",fljB_First_Choice,fljB_Sec_Choice,fljB_Third_Choice)
+  print "$$_H:No fliC, only fljB, and its order:",fljB_First_Choice,fljB_Sec_Choice,fljB_Third_Choice
 elif score==1 and fljB_score>100:
-  print("$$_H:No fliC (file) existed, only fljB, and its order:",fljB_First_Choice,fljB_Sec_Choice,fljB_Third_Choice)
+  print "$$_H:No fliC (file) existed, only fljB, and its order:",fljB_First_Choice,fljB_Sec_Choice,fljB_Third_Choice
 elif score==1 and fljB_score<100:
-  print("$$_H:No fliC (file) existed, and no fljB")
+  print "$$_H:No fliC (file) existed, and no fljB"
 elif score>100 and fljB_score==1:
-  print("$$_H:No fljB (file) existed, only fliC, and its order:",First_Choice,Sec_Choice,Third_Choice)
+  print "$$_H:No fljB (file) existed, only fliC, and its order:",First_Choice,Sec_Choice,Third_Choice
 elif score<100 and fljB_score==1:
-  print("$$_H:No fljB (file) existed, and no fliC")
+  print "$$_H:No fljB (file) existed, and no fliC"
 else:
-  print("$$_H:No fliC and fljB")
+  print "$$_H:No fliC and fljB"
 
 
 '''
diff -r acc5cd06a36a -r 53efef402c51 libs/Otype_determine_analysis.py
--- a/libs/Otype_determine_analysis.py	Tue Nov 28 21:16:36 2017 -0500
+++ b/libs/Otype_determine_analysis.py	Wed Nov 29 08:34:19 2017 -0500
@@ -49,17 +49,17 @@
               O_2_score=O_2_score+hsp.bits
     if O_9_score>100:
       if O_9_score>O_2_score:
-        print('$$$ Most possible O_type: O-9','\n')
-        print('$$$ longest_bit_score:',O_9_score,'\n')
+        print '$$$ Most possible O_type: O-9','\n'
+        print '$$$ longest_bit_score:',O_9_score,'\n'
       else:
-        print('$$$ Most possible O_type: O-2','\n')
-        print('$$$ longest_bit_score:',O_2_score,'\n')
+        print '$$$ Most possible O_type: O-2','\n'
+        print '$$$ longest_bit_score:',O_2_score,'\n'
     else:
-      print("Assumpition wrong, no O2 or O9, return to re-analysis")
+      print "Assumpition wrong, no O2 or O9, return to re-analysis"
       if ('O-2_' not in Sec_Choice) and ('O-9_' not in Sec_Choice):
-        print('$$$ Most possible O_type Choice (no tyr difference):',Sec_Choice)
+        print '$$$ Most possible O_type Choice (no tyr difference):',Sec_Choice
       if (('O-2_' in Sec_Choice) or ('O-9_' in Sec_Choice)) and ('O-2_' not in Third_Choice) and ('O-9_' not in Third_Choice):
-          print('$$$ Most possible O_type Choice (no tyr difference):',Third_Choice)
+          print '$$$ Most possible O_type Choice (no tyr difference):',Third_Choice
     os.system("rm tyr_of_O2_O9.fasta_db.*")###01/28/2015
     os.system("rm "+xml_file)###01/28/2015
   if subdatabase=="oafA_of_O4_O5.fasta":
@@ -76,17 +76,17 @@
                 O_2_score=O_2_score+hsp.bits
       if O_9_score>100:
         if O_9_score>O_2_score:
-          print('$$$O5_none_7_base_deletion','\n')
-          print('$$$ longest_bit_score:',O_9_score,'\n')
+          print '$$$O5_none_7_base_deletion','\n'
+          print '$$$ longest_bit_score:',O_9_score,'\n'
         else:
-          print('$$$O5-','\n'
-          print('$$$ longest_bit_score:',O_2_score,'\n')
+          print '$$$O5-','\n'
+          print '$$$ longest_bit_score:',O_2_score,'\n'
       else:
-        print('$$$O5_none_7_base_deletion,unsure','\n')
+        print '$$$O5_none_7_base_deletion,unsure','\n'
       os.system("rm oafA_of_O4_O5.fasta_db.*")###01/28/2015
       os.system("rm "+xml_file)###01/28/2015
     except:
-      print("No oafA genes")
+      print "No oafA genes"
   if subdatabase=="O_3,10_and_1,3,19_spe.fasta":
     try:
       for record in records:    #there are many records (i.e. the '>' in query file), so change another method
@@ -101,16 +101,16 @@
                 O_2_score=O_2_score+hsp.bits
       if O_9_score>200:
         if O_9_score>O_2_score:
-          print('$$$O3,10 more possible','\n'
-          print('$$$ longest_bit_score:',O_9_score,'\n'
+          print '$$$O3,10 more possible','\n'
+          print '$$$ longest_bit_score:',O_9_score,'\n'
       else:
         if O_2_score>100:
-          print('$$$O1,3,19 more possible','\n'
-          print('$$$ longest_bit_score:',O_2_score,'\n'
+          print '$$$O1,3,19 more possible','\n'
+          print '$$$ longest_bit_score:',O_2_score,'\n'
       os.system("rm O_3,10_and_1,3,19_spe.fasta_db.*")###01/28/2015
       os.system("rm "+xml_file)###01/28/2015
     except:
-      print("No O3,10_and_O1,3,19 spe sequences"
+      print "No O3,10_and_O1,3,19 spe sequences"
 
 
 def show_result():
@@ -231,25 +231,25 @@
         else:
           names=First_Choice+Sec_Choice
         if score==0:
-          print("$$$ No O_type, due to no hit of rfb")
+          print "$$$ No O_type, due to no hit of rfb"
           names=""
         if 'O-2_' in names and 'O-9_' in names and ('O-2_' in First_Choice or 'O-9_' in First_Choice):
-          print('#Contain O2 and O9, so change to special test')
+          print '#Contain O2 and O9, so change to special test'
           test_O29("tyr_of_O2_O9.fasta")
         else:
           if score>0:
-            print('$$$ Most possible O_type: ',First_Choice,'\n')
-            print('$$$ Most bit_score:',score,'\n')
+            print '$$$ Most possible O_type: ',First_Choice,'\n'
+            print '$$$ Most bit_score:',score,'\n'
             if "O-4_" in First_Choice:#$$$$$$$
               test_O29("oafA_of_O4_O5.fasta")#$$$$$$$
             if "O-1,3,19" in First_Choice or "O-3,10" in First_Choice:
               test_O29("O_3,10_and_1,3,19_spe.fasta")#$$$$$$$
           if secscore>0:
-            print('$$$ Second possible O_type: ',Sec_Choice,'\n')
-            print('$$$ Second bit_score:',secscore,'\n')
+            print '$$$ Second possible O_type: ',Sec_Choice,'\n'
+            print '$$$ Second bit_score:',secscore,'\n'
           if thirdscore>0:
-            print('$$$ Third possible O_type: ',Third_Choice,'\n'
-            print('$$$ Third bit_score:',thirdscore,'\n')
+            print '$$$ Third possible O_type: ',Third_Choice,'\n'
+            print '$$$ Third bit_score:',thirdscore,'\n'
 
 
 
@@ -261,13 +261,13 @@
 target=sys.argv[2]
 database=sys.argv[3]
 output=target.split('.')[0]+'_out.fa'
-print("$$:",target
+print "$$:",target
 
 
 os.system(Makebltdb+' -in '+target+' -out '+target+'_db '+'-dbtype nucl')###01/28/2015
 os.system(Blastnpth+' -query '+queries+' -db '+target+'_db '+'-out '+queries+'_vs_'+target+'.xml '+'-outfmt 5')###01/28/2015, since it's abs address for "run_auto*.py", so no need to change "query" address this time
 xml_file=queries+'_vs_'+target+'.xml'
-print('\n'
+print '\n'
 result_handle=open(xml_file)
 blast_record=NCBIXML.parse(result_handle)
 blast_record=list(blast_record)
@@ -277,13 +277,13 @@
 #os.system("rm "+target+'_db.*')###01/28/2015
 
 if len(blast_record)==2:
-  print('Hits have been got'+'\n')
+  print 'Hits have been got'+'\n'
   if len(blast_record[0].alignments)==1 and len(blast_record[1].alignments)==1:
-    print('Checking the number of alignments:  2 alignments obtained'+'\n')
+    print 'Checking the number of alignments:  2 alignments obtained'+'\n'
     if len(blast_record[0].alignments[0].hsps)==1 and len(blast_record[1].alignments[0].hsps)==1:
-      print('Checking the number of hsps:  each alignment has 1 hsp'+'\n')
+      print 'Checking the number of hsps:  each alignment has 1 hsp'+'\n'
       if blast_record[0].alignments[0].hit_def==blast_record[1].alignments[0].hit_def:
-        print('Checking locations of hits:  Both hits are located in '+'"'+str(blast_record[0].alignments[0].hit_def)+'"'+'...'+'\n')
+        print 'Checking locations of hits:  Both hits are located in '+'"'+str(blast_record[0].alignments[0].hit_def)+'"'+'...'+'\n'
                
         hit_1_start=blast_record[0].alignments[0].hsps[0].sbjct_start
         hit_1_end=blast_record[0].alignments[0].hsps[0].sbjct_end
@@ -301,11 +301,11 @@
           hit_2_start=hit_2_end
           hit_2_end=buffer
 
-        print('hit_1_start: '+str(hit_1_start)
-        print('hit_1_end: '+str(hit_1_end)
+        print 'hit_1_start: '+str(hit_1_start)
+        print 'hit_1_end: '+str(hit_1_end)
 
-        print('hit_2_start: '+str(hit_2_start)
-        print('hit_2_end: '+str(hit_2_end)
+        print 'hit_2_start: '+str(hit_2_start)
+        print 'hit_2_end: '+str(hit_2_end)
 
     
         if hit_1_end<hit_2_start:                    
@@ -315,15 +315,15 @@
           extract_start=hit_2_end+1
           extract_end=hit_1_start-1
                   
-        print('start: '+str(extract_start), 'end: '+str(extract_end)+'\n')
+        print 'start: '+str(extract_start), 'end: '+str(extract_end)+'\n'
 
         for contig in target_seq:
           if (contig.description==blast_record[0].alignments[0]) or (contig.description.replace(" ","")==blast_record[0].alignments[0].hit_def.replace(" ","")):
             target_contig=contig
 
         rfb_region=target_contig[extract_start:extract_end]
-        print('Extracted rfb region length:  '+str(len(rfb_region.seq.tostring()))+'\n')
-        print('Extracted rfb region saved in:  '+output+'\n')
+        print 'Extracted rfb region length:  '+str(len(rfb_region.seq.tostring()))+'\n'
+        print 'Extracted rfb region saved in:  '+output+'\n'
 
         outfile=open(output,'w')
         title='>'+target.split('.')[0]+' rfb region:'+blast_record[0].alignments[0].hit_def+':'+str(extract_start)+' to '+str(extract_end)+'_'+str(len(rfb_region.seq.tostring()))+'bp'+')'
@@ -336,7 +336,7 @@
         os.system(Makebltdb+' -in '+database+' -out '+database+'_db '+'-dbtype nucl')
         os.system(Blastnpth+' -query '+output+' -db '+database+'_db '+'-out '+'Blast_Otype_'+target+'.xml '+'-outfmt 5')
         xml_file='Blast_Otype_'+target+'.xml'
-        print('\n'
+        print '\n'
 
 
         filehandle=open(xml_file)
@@ -349,7 +349,7 @@
         show_result()
 
       else:
-        print('Checking locations of hits:  the two hits are not located in same contig......'+'\n')
+        print 'Checking locations of hits:  the two hits are not located in same contig......'+'\n'
         hit_1_start=blast_record[0].alignments[0].hsps[0].sbjct_start
         hit_1_end=blast_record[0].alignments[0].hsps[0].sbjct_end
         hit_2_start=blast_record[1].alignments[0].hsps[0].sbjct_start
@@ -400,7 +400,7 @@
         os.system(Makebltdb+' -in '+database+' -out '+database+'_db '+'-dbtype nucl')
         os.system(Blastnpth+' -query '+output+' -db '+database+'_db '+'-out '+'Blast_Otype_'+target+'.xml '+'-outfmt 5')
         xml_file='Blast_Otype_'+target+'.xml'
-        print('\n')
+        print '\n'
 
 
         filehandle=open(xml_file)
@@ -431,7 +431,7 @@
                 
         os.system(Blastnpth+' -query combined_sequence.fasta'+' -db '+database+'_db '+'-out '+'Combined_seq_blast_'+target+'.xml '+'-outfmt 5')
         xml_file='Combined_seq_blast_'+target+'.xml'
-        print('\n'
+        print '\n'
 
         filehandle=open(xml_file)
         records=NCBIXML.parse(filehandle)
@@ -443,18 +443,18 @@
         
 
     else:
-      print('$$$ No O_type result, please check the number of hsps:  some alignment have more than 1 hsp (galF or gnd sequences has one more hits in tested genome), that\'s unusual for for our short sequence gnd and galF, please check your submited sequence'+'\n'
+      print '$$$ No O_type result, please check the number of hsps:  some alignment have more than 1 hsp (galF or gnd sequences has one more hits in tested genome), that\'s unusual for for our short sequence gnd and galF, please check your submited sequence'+'\n'
      
           
   elif len(blast_record[0].alignments)>1 and len(blast_record[1].alignments)==1:
-    print('The gnd gene is splited on different contigs of your submitted sequence' +'\n'
+    print 'The gnd gene is splited on different contigs of your submitted sequence' +'\n'
     for record in blast_record:
       for alignment in record.alignments:
         if len(alignment.hsps)!=1:
-          print('$$$ No O_type result, please check the number of hsp:  some alignment have more than 1 hsp (galF or gnd sequences has one more hits in tested genome), that\'s unusual for our short sequence gnd and galF, please check your submited sequence'+'\n'
+          print '$$$ No O_type result, please check the number of hsp:  some alignment have more than 1 hsp (galF or gnd sequences has one more hits in tested genome), that\'s unusual for our short sequence gnd and galF, please check your submited sequence'+'\n'
           break
         
-    print('Each alignment has one hsps'+'\n'
+    print 'Each alignment has one hsps'+'\n'
      
 
                 
@@ -515,12 +515,12 @@
 
     os.system(Makebltdb+' -in '+database+' -out '+database+'_db '+'-dbtype nucl')
     os.system(Blastnpth+' -query '+output+' -db '+database+'_db '+'-out '+'Blast_Otype_'+target+'.xml '+'-outfmt 5')
-    print('\n')
+    print '\n'
     xml_file2='Blast_Otype_'+target+'.xml'
     filehandle=open(xml_file2)
     records=NCBIXML.parse(filehandle)
     records=list(records)
-    print(len(records))
+    print len(records)
     realrecord1=records[0]
     if len(records[1].alignments)>len(records[0].alignments):
       realrecord1=records[1]
@@ -548,7 +548,7 @@
                 
     os.system(Blastnpth+' -query combined_sequence.fasta'+' -db '+database+'_db '+'-out '+'Combined_seq_blast_'+target+'.xml '+'-outfmt 5')
     xml_file='Combined_seq_blast_'+target+'.xml'
-    print('\n')
+    print '\n'
 
 
     filehandle=open(xml_file)
@@ -560,14 +560,14 @@
 
 
   elif len(blast_record[0].alignments)==1 and len(blast_record[1].alignments)>1:
-    print('The galF gene is splited on different contigs of your submitted sequence' +'\n')
+    print 'The galF gene is splited on different contigs of your submitted sequence' +'\n'
     for record in blast_record:
       for alignment in record.alignments:
         if len(alignment.hsps)!=1:
-          print('$$$ No O_type result, please check the number of hsps:  some alignment have more than 1 hsp (galF or gnd sequences has one more hits in tested genome), that\'s unusual for our short sequence gnd and galF, please check your submited sequence'+'\n')
+          print '$$$ No O_type result, please check the number of hsps:  some alignment have more than 1 hsp (galF or gnd sequences has one more hits in tested genome), that\'s unusual for our short sequence gnd and galF, please check your submited sequence'+'\n'
           break
         
-    print('Each alignment has one hsp'+'\n')                 
+    print 'Each alignment has one hsp'+'\n'                 
     outfile=open(output,'w')
 
     for alignment in blast_record[0].alignments:
@@ -622,7 +622,7 @@
 
     os.system(Makebltdb+' -in '+database+' -out '+database+'_db '+'-dbtype nucl')
     os.system(Blastnpth+' -query '+output+' -db '+database+'_db '+'-out '+'Blast_Otype_'+target+'.xml '+'-outfmt 5')
-    print('\n')
+    print '\n'
     xml_file='Blast_Otype_'+target+'.xml'
     filehandle=open(xml_file)
     records=NCBIXML.parse(filehandle)
@@ -654,7 +654,7 @@
                 
     os.system(Blastnpth+' -query combined_sequence.fasta'+' -db '+database+'_db '+'-out '+'Combined_seq_blast_'+target+'.xml '+'-outfmt 5')
     xml_file='Combined_seq_blast_'+target+'.xml'
-    print('\n')
+    print '\n'
 
 
     filehandle=open(xml_file)
@@ -665,14 +665,14 @@
      
 
   elif len(blast_record[0].alignments)>1 and len(blast_record[1].alignments)>1:
-    print('The gnd and galF gene are both splited on different contigs of your submitted sequence' +'\n')
+    print 'The gnd and galF gene are both splited on different contigs of your submitted sequence' +'\n'
     for record in blast_record:
       for alignment in record.alignments:
         if len(alignment.hsps)!=1:
-          print('$$$ No O_type result, please check the number of hsp:  some alignment have more than 1 hsp (galF or gnd sequences has one more hits in tested genome), that\'s unusual for our short sequence gnd and galF, please check your submited sequence'+'\n')
+          print '$$$ No O_type result, please check the number of hsp:  some alignment have more than 1 hsp (galF or gnd sequences has one more hits in tested genome), that\'s unusual for our short sequence gnd and galF, please check your submited sequence'+'\n'
           break
         
-    print('Each alignment has one hsps'+'\n')
+    print 'Each alignment has one hsps'+'\n'
     outfile=open(output,'w')
 
     for alignment in blast_record[0].alignments:
@@ -728,7 +728,7 @@
     os.system(Makebltdb+' -in '+database+' -out '+database+'_db '+'-dbtype nucl')
     os.system(Blastnpth+' -query '+output+' -db '+database+'_db '+'-out '+'Blast_Otype_'+target+'.xml '+'-outfmt 5')
     xml_file='Blast_Otype_'+target+'.xml'
-    print('\n')
+    print '\n'
     filehandle=open(xml_file)
     records=NCBIXML.parse(filehandle)
     records=list(records)
@@ -759,7 +759,7 @@
                 
     os.system(Blastnpth+' -query combined_sequence.fasta'+' -db '+database+'_db '+'-out '+'Combined_seq_blast_'+target+'.xml '+'-outfmt 5')
     xml_file='Combined_seq_blast_'+target+'.xml'
-    print('\n')
+    print '\n'
 
 
     filehandle=open(xml_file)
@@ -771,7 +771,7 @@
 
 
 else:
-  print('$$$ $$$ No O_type result, Attention: unusual number of hits, no hits for galF or gnd! Check blast output...'+'\n')
+  print '$$$ $$$ No O_type result, Attention: unusual number of hits, no hits for galF or gnd! Check blast output...'+'\n'
 
 
 os.system('rm '+target+'_db.'+'*')
diff -r acc5cd06a36a -r 53efef402c51 libs/compare_and_change_two_fastq_id.py
--- a/libs/compare_and_change_two_fastq_id.py	Tue Nov 28 21:16:36 2017 -0500
+++ b/libs/compare_and_change_two_fastq_id.py	Wed Nov 29 08:34:19 2017 -0500
@@ -17,11 +17,11 @@
   if a_title==b_title:
     pass
   else:
-    print("changing the title of two seperated fastq files...")
-    print(a_title,b_title)
+    print "changing the title of two seperated fastq files..."
+    print a_title,b_title
     os.system("sed "+"-i 's/.1 / /g' "+file1)
-    print("finished file1")
+    print "finished file1"
     os.system("sed "+"-i 's/.2 / /g' "+file2)
-    print("finished file2")
+    print "finished file2"
 
 compare_and_change_two_fastq_id(file1,file2) 
\ No newline at end of file
diff -r acc5cd06a36a -r 53efef402c51 libs/deletion_compare.py
--- a/libs/deletion_compare.py	Tue Nov 28 21:16:36 2017 -0500
+++ b/libs/deletion_compare.py	Wed Nov 29 08:34:19 2017 -0500
@@ -120,15 +120,15 @@
         O2_bigger+=1
     except:
       continue
-  print("$$$Genome:",sra_name)
+  print "$$$Genome:",sra_name
   if O9_bigger>O2_bigger:
-    print("$$$Typhimurium")
+    print "$$$Typhimurium"
   elif O9_bigger<O2_bigger:
-    print("$$$Typhimurium_O5-")
+    print "$$$Typhimurium_O5-"
   else:
-    print("$$$Typhimurium, even no 7 bases difference")
-  print("O-4 number is:",O9_bigger)
-  print("O-4_5- number is:",O2_bigger)
+    print "$$$Typhimurium, even no 7 bases difference"
+  print "O-4 number is:",O9_bigger
+  print "O-4_5- number is:",O2_bigger
   os.system("rm "+sam+"_title.txt")###01/28/2015
   os.system("rm "+sam+"_seq.txt")###01/28/2015
   os.system("rm "+sam+".fasta")###01/28/2015
diff -r acc5cd06a36a -r 53efef402c51 libs/run_auto_All_for_assemblies.py
--- 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")
   '''
 
diff -r acc5cd06a36a -r 53efef402c51 libs/run_auto_All_for_web_multi_revise.py
--- a/libs/run_auto_All_for_web_multi_revise.py	Tue Nov 28 21:16:36 2017 -0500
+++ b/libs/run_auto_All_for_web_multi_revise.py	Wed Nov 29 08:34:19 2017 -0500
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python2.7
 
 
 
@@ -63,16 +63,16 @@
     additional_file=file2
   except:
     pass
-  #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, because we add one directory to the result directory
   if file_mode=="1":
-    os.system('python '+dirpath+'/BWA_analysis_O_new_dependent.py '+real_file+' '+database_path+'/special_new_O_genes.fasta '+mapping_mode+' 1 >temp_result_'+str(q)+'O.txt')###01/27/2015
+    os.system('python2.7 '+dirpath+'/BWA_analysis_O_new_dependent.py '+real_file+' '+database_path+'/special_new_O_genes.fasta '+mapping_mode+' 1 >temp_result_'+str(q)+'O.txt')###01/27/2015
   elif file_mode=="2":
-    os.system('python '+dirpath+'/BWA_analysis_O_new_dependent.py '+real_file+' '+database_path+'/special_new_O_genes.fasta '+mapping_mode+" "+additional_file+' 2 >temp_result_'+str(q)+'O.txt')###01/27/2015
+    os.system('python2.7 '+dirpath+'/BWA_analysis_O_new_dependent.py '+real_file+' '+database_path+'/special_new_O_genes.fasta '+mapping_mode+" "+additional_file+' 2 >temp_result_'+str(q)+'O.txt')###01/27/2015
   elif file_mode=="3":
-    os.system('python '+dirpath+'/BWA_analysis_O_new_dependent.py '+real_file+' '+database_path+'/special_new_O_genes.fasta '+mapping_mode+' 3 >temp_result_'+str(q)+'O.txt')###01/27/2015
+    os.system('python2.7 '+dirpath+'/BWA_analysis_O_new_dependent.py '+real_file+' '+database_path+'/special_new_O_genes.fasta '+mapping_mode+' 3 >temp_result_'+str(q)+'O.txt')###01/27/2015
   os.system('cat temp_result_'+str(q)+'O.txt>>data_log.txt')###01/28/2015
   handle=open('temp_result_'+str(q)+'O.txt',"r")
   handle=handle.readlines()
@@ -92,11 +92,11 @@
   if sdf!="+":#
     sdf="-"#
   if file_mode=="1":
-    os.system('python '+dirpath+'/BWA_analysis_H_update_new_family_dependent.py '+real_file+' '+database_path+'/H_combine_update_9_03_2014_new.fasta '+mapping_mode+' 1 >temp_result_'+str(q)+'H.txt')###01/27/2015
+    os.system('python2.7 '+dirpath+'/BWA_analysis_H_update_new_family_dependent.py '+real_file+' '+database_path+'/H_combine_update_9_03_2014_new.fasta '+mapping_mode+' 1 >temp_result_'+str(q)+'H.txt')###01/27/2015
   if file_mode=="2":
-    os.system('python '+dirpath+'/BWA_analysis_H_update_new_family_dependent.py '+real_file+" "+database_path+'/H_combine_update_9_03_2014_new.fasta '+mapping_mode+' '+additional_file+' 2 >temp_result_'+str(q)+'H.txt')###01/27/2015
+    os.system('python2.7 '+dirpath+'/BWA_analysis_H_update_new_family_dependent.py '+real_file+" "+database_path+'/H_combine_update_9_03_2014_new.fasta '+mapping_mode+' '+additional_file+' 2 >temp_result_'+str(q)+'H.txt')###01/27/2015
   if file_mode=="3":
-    os.system('python '+dirpath+'/BWA_analysis_H_update_new_family_dependent.py '+real_file+' '+database_path+'/H_combine_update_9_03_2014_new.fasta '+mapping_mode+' 3 >temp_result_'+str(q)+'H.txt')###01/27/2015
+    os.system('python2.7 '+dirpath+'/BWA_analysis_H_update_new_family_dependent.py '+real_file+' '+database_path+'/H_combine_update_9_03_2014_new.fasta '+mapping_mode+' 3 >temp_result_'+str(q)+'H.txt')###01/27/2015
   os.system('cat temp_result_'+str(q)+'H.txt>>data_log.txt')
   handle2=open('temp_result_'+str(q)+'H.txt',"r")
   handle2=handle2.readlines()
@@ -176,18 +176,18 @@
   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:-":#
@@ -216,11 +216,11 @@
   '''
   if "Typhimurium" in predict_sero or predict_form=="4:i:-":#03252016#
     if file_mode=="1":
-      os.system('python '+dirpath+'/deletion_compare.py '+real_file+' oafA '+mapping_mode+' 1 >temp_result_'+str(q)+'Typhim.txt')###02/06/2015
+      os.system('python2.7 '+dirpath+'/deletion_compare.py '+real_file+' oafA '+mapping_mode+' 1 >temp_result_'+str(q)+'Typhim.txt')###02/06/2015
     if file_mode=="2":
-      os.system('python '+dirpath+'/deletion_compare.py '+real_file+' oafA '+mapping_mode+" "+additional_file+' 2 >temp_result_'+str(q)+'Typhim.txt')###02/06/2015
+      os.system('python2.7 '+dirpath+'/deletion_compare.py '+real_file+' oafA '+mapping_mode+" "+additional_file+' 2 >temp_result_'+str(q)+'Typhim.txt')###02/06/2015
     if file_mode=="3":
-      os.system('python '+dirpath+'/deletion_compare.py '+real_file+' oafA '+mapping_mode+' 3 >temp_result_'+str(q)+'Typhim.txt')###02/06/2015
+      os.system('python2.7 '+dirpath+'/deletion_compare.py '+real_file+' oafA '+mapping_mode+' 3 >temp_result_'+str(q)+'Typhim.txt')###02/06/2015
     os.system('cat temp_result_'+str(q)+'Typhim.txt>>data_log.txt')###01/28/2015
     handle=open('temp_result_'+str(q)+'Typhim.txt',"r")
     handle=handle.readlines()
@@ -299,16 +299,16 @@
     for j in xrange(len(jobs)):
       jobs[j].join()
       txt_names.append(file_names[j+i].replace(' ','_').replace(":","__").replace("[","").replace("]","")+".txt")
-    print(txt_names)
+    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
 
-  print("End time,",time.time())
+  print "End time,",time.time()
 '''
 
 if __name__ == '__main__':
diff -r acc5cd06a36a -r 53efef402c51 libs/special_gene_test_assemblies.py
--- a/libs/special_gene_test_assemblies.py	Tue Nov 28 21:16:36 2017 -0500
+++ b/libs/special_gene_test_assemblies.py	Wed Nov 29 08:34:19 2017 -0500
@@ -31,7 +31,7 @@
     for record in records:
       for alignment in record.alignments:
         if x in alignment.hit_def: #multi gene database, so...
-          print(x,"got a hit, evaluating the hit quality...")
+          print x,"got a hit, evaluating the hit quality..."
           score=0
           for hsp in alignment.hsps:
             if hsp.expect<E_thresh:
@@ -46,9 +46,9 @@
         First_Choice=Htype
         score=scorelist[Htype]
     if float(score)>=0.1*aver_len:
-      print("$$$",First_Choice,"got a hit, score:",score)
+      print "$$$",First_Choice,"got a hit, score:",score
     else:
-      print("$$$No ",x,"exists")
+      print "$$$No ",x,"exists"
   os.system("rm "+database+"_db.*")##########1/28/2015
   os.system("rm "+xml_file)##########1/28/2015
 
diff -r acc5cd06a36a -r 53efef402c51 run_seqsero.py
--- a/run_seqsero.py	Tue Nov 28 21:16:36 2017 -0500
+++ b/run_seqsero.py	Wed Nov 29 08:34:19 2017 -0500
@@ -96,9 +96,9 @@
         for run in run2fastqs:
                 seqsero_cmd = []
                 if len(run2fastqs[run]) == 2:
-                        seqsero_cmd = ['python', seqsero, '-m', '2', '-i', run2fastqs[run][0], run2fastqs[run][1]]
+                        seqsero_cmd = ['python2.7', seqsero, '-m', '2', '-i', run2fastqs[run][0], run2fastqs[run][1]]
                 elif len(run2fastqs[run]) == 1:
-                        seqsero_cmd = ['python', seqsero, '-m', '1', '-i', run2fastqs[run][0]]
+                        seqsero_cmd = ['python2,7', seqsero, '-m', '1', '-i', run2fastqs[run][0]]
                 p = Popen(seqsero_cmd, stdout=PIPE)
                 output = p.communicate()
                 outputs.append(output)
diff -r acc5cd06a36a -r 53efef402c51 seqsero.xml
--- a/seqsero.xml	Tue Nov 28 21:16:36 2017 -0500
+++ b/seqsero.xml	Wed Nov 29 08:34:19 2017 -0500
@@ -12,9 +12,9 @@
                 <exit_code range="0:" level="warning"/>
                 <regex match="Error:"/>
         </stdio>
-        <command>
+        <command interpreter="python2.7">
      
-                python $__tool_directory__/run_seqsero.py $input1 $__tool_directory__/
+               $__tool_directory__/run_seqsero.py $input1 $__tool_directory__/
                 
         </command> 
         <inputs>
diff -r acc5cd06a36a -r 53efef402c51 test.txt
--- a/test.txt	Tue Nov 28 21:16:36 2017 -0500
+++ b/test.txt	Wed Nov 29 08:34:19 2017 -0500
@@ -3,6 +3,22 @@
 /galaxydir/galaxy/tools/GalaxySeqsero/run_seqsero.py	/galaxydir/galaxy/database/files/000/dataset_170.dat,/galaxydir/galaxy/database/files/000/dataset_171.dat	/galaxydir/galaxy/tools/GalaxySeqsero/
 3
 2
-b"('\\n', '\\n')\nInput files:\tdataset_170_SRR6325381.fastq dataset_171_SRR6325381.fastq\nO antigen prediction:\tO-?\nH1 antigen prediction(fliC):\t-\nH2 antigen prediction(fljB):\t1,6\nPredicted antigenic profile:\t?:-:1,6\nPredicted serotype(s):\tN/A (The predicted antigenic profile does not exist in the White-Kauffmann-Le Minor scheme)\n\ncheck fastq id and make them in accordance with each other...please wait...\n\n\n\nResult:\n\n"
+
+
+
+Input files:	dataset_170_SRR6325381.fastq dataset_171_SRR6325381.fastq
+O antigen prediction:	O-3,10
+H1 antigen prediction(fliC):	e,h
+H2 antigen prediction(fljB):	1,6
+Predicted antigenic profile:	3,10:e,h:1,6
+Predicted serotype(s):	Anatum
+The serotype(s) is/are the only serotype(s) with the indicated antigenic profile currently recognized in the Kauffmann White Scheme.  New serotypes can emerge and the possibility exists that this antigenic profile may emerge in a different subspecies.  Identification of strains to the subspecies level should accompany serotype determination; the same antigenic profile in different subspecies is considered different serotypes.
+check fastq id and make them in accordance with each other...please wait...
+
+
+
+Result:
+
+
 None
-Tue Nov 28 19:30:26 2017
\ No newline at end of file
+Wed Nov 29 07:50:31 2017
\ No newline at end of file