Mercurial > repos > estrain > seqsero2_v1_0_1

changeset 19:e33565b4610c

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Uploaded
author estrain
date Sat, 07 Sep 2019 13:16:43 -0400
parents e1287b36e0d3
children b2b1d018b90d
files SeqSero2_package.py
diffstat 1 files changed, 2 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- a/SeqSero2_package.py	Sat Sep 07 13:11:54 2019 -0400
+++ b/SeqSero2_package.py	Sat Sep 07 13:16:43 2019 -0400
@@ -1217,11 +1217,13 @@
   salmID_output=subprocess.Popen(dirpath+"/SalmID.py -i "+fnameA,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE)
   out, err = salmID_output.communicate()
   out=out.decode("utf-8")
+  err=err.decode("utf-8")
   file=open("data_log.txt","a")
   file.write(out)
   file.close()
   print("dirpath " + str(dirpath))
   print("SalmID File" + str(out))
+  print("SalmID Err File" + str(err))
   print("SalmID 1 "+str(out.split("\n")[1]))
   print("SalmID 0 "+str(out.split("\n")[0]))
   salm_species_scores=out.split("\n")[1].split("\t")[6:]