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

planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty

--- 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