diff libs/BWA_analysis_O_new_dependent.py @ 7:3d6680af0bec draft

planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty

--- a/libs/BWA_analysis_O_new_dependent.py	Mon Nov 27 14:37:41 2017 -0500
+++ b/libs/BWA_analysis_O_new_dependent.py	Mon Nov 27 16:30:27 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