diff bin/SeqSero2_package.py @ 10:e6437d423693 draft

planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty

--- a/bin/SeqSero2_package.py	Thu Apr 30 21:47:42 2020 -0400
+++ b/bin/SeqSero2_package.py	Fri May 01 13:30:43 2020 -0400
@@ -1236,12 +1236,14 @@
 def judge_subspecies(fnameA,dirpath):
   #seqsero2 -a; judge subspecies on just forward raw reads fastq
   samid_strcmd = "python " + dirpath + "/../SalmID.py -i "+fnameA
-  #subprocess.check_call(samid_strcmd + " > Salmidoutput.txt",shell=True)
   print(samid_strcmd)
+  #seqsero2 -a; judge subspecies on just forward raw reads fastq
+  #salmID_output=subprocess.Popen("SalmID.py -i "+fnameA,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE)
   salmID_output=subprocess.Popen(samid_strcmd,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE)
   out, err = salmID_output.communicate()
-  print("judge_subspecies -> err = salmID_output.communicate() " + err)
   out=out.decode("utf-8")
+  print(out)
+  print(err)
   file=open("data_log.txt","a")
   file.write(out)
   file.close()